from:"Tanner, John J."

Re: [ccp4bb] Database for submitting unprocessed diffraction data

2023-10-18 Thread Tanner, John J.

You could try https://www.proteindiffraction.org/

From: CCP4 bulletin board  on behalf of JEROME JOHNSON 

Date: Wednesday, October 18, 2023 at 11:33 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Database for submitting unprocessed diffraction data
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Hello all,

As the subject says, I am looking for an open online database to store 
unprocessed diffraction data.  Does such a database exist? Essentially we would 
like our diffracted data to be freely available online while also outsourcing 
some of our data management.

Any advice would be wonderful!

Best,
Jerome

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Re: [ccp4bb] Crystallization Robots

2022-05-23 Thread Tanner, John J.

I would like to echo the good things that have been said about the Oryx8. We 
bought one in 2016 and it has been essentially trouble-free. The instrument is 
used by multiple people from different labs, including undergrads, graduate 
students, and postdocs. Robustness and ease-of-use are essential in multiuser, 
academic environments, and the Oryx8 has proven to be a robust instrument that 
seems unbreakable. The few issues we have had, like alignment problems or the 
drops not getting set correctly, were solved quickly via email support from 
Douglas. Support from Douglas has been outstanding. Stefan always replies fast 
and sometimes Patrick provides help. Another big plus of the Oryx8 is low 
consumable costs.

In summary, I have two crystallization robots in my lab and only one of them is 
operational – the Oryx8.


From: CCP4 bulletin board  on behalf of Shawn Rumrill 

Date: Monday, May 23, 2022 at 9:12 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Crystallization Robots
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Hello,

Does anyone have experience with either the Oryx8 or Formulatrix NT8 for 
setting up crystallization trays? Both instruments look very capable on paper. 
I am looking for something that is easy to use, robust, and can handle a 
variety of different crystallization experiments (screening and optimization). 
What do you like/dislike about either system?

Thanks for your insights!

Shawn



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[ccp4bb] Fragment-based drug discovery session at ACA 2022

2022-04-08 Thread Tanner, John J.

As many of you know, the 2022 ACA meeting will be held in Portland, OR on July 
29 to August 2. I would like to draw your attention to the session on 
fragment-based drug discovery and invite you to submit an abstract for an oral 
presentation. We welcome contributions from students as well as PIs. The 
Abstract deadline is April 15.

https://www.acameeting.com/

Session details:

3.2.2 Fragment Based Drug Discovery
8/1/2022 @ 2:00:00 PM - 5:00:00 PM
Sponsoring SIG(s): Industrial
Co-Sponsoring SIG(s): BioMac
Session Chair(s): Matt Clifton, Jack Tanner
Fragment Based Drug Discovery (FBDD) utilizes small molecule compounds to help 
identify starting points in the drug discovery process. This process allowed 
for the discovery of lead compounds for difficult protein targets with 
small/shallow pockets or protein-protein interactions. In contrast to other 
screening techniques such as High-Throughput Screening (HTS) or DNA-encoded 
Libraries (DEL), FBDD utilizes small libraries of molecules (< 2000) with 
molecular weights less than ~200 Da. FBDD has been key in the development of 
multiple approved drugs and dozens of other drugs in clinical trials. This 
session will focus on the biophysical and structural techniques used in FBDD to 
identify initial starting points, optimization by fragment growing/linking, and 
the route to lead optimization.

--
John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu
https://cafnrfaculty.missouri.edu/tannerlab/
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A





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Re: [ccp4bb] Strategies for increasing Trp content of proteins

2022-02-19 Thread Tanner, John J.

Casper: You make a good point about using 205 nm. I checked our system this 
morning and the wavelength is fixed at 280 nm (U9-L).

Artem: Did you consider secondary structure and/or amino acid residue type when 
choosing sites for mutagenesis? Is your work published?

From: CCP4 bulletin board  on behalf of Casper Wilkens 
<5d34ab0aef35-dmarc-requ...@jiscmail.ac.uk>
Date: Saturday, February 19, 2022 at 2:19 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Sv: [ccp4bb] Strategies for increasing Trp content of proteins
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Is absorbance at 205 nm not a possibility, Jack?

Casper Wilkens
Asst. Prof.
Structural Enzymology & Biorefining
DTU Bioengineering

Technical University of Denmark
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Fra: CCP4 bulletin board  på vegne af Artem Evdokimov 

Sendt: 19. februar 2022 02:12:50
Til: CCP4BB@JISCMAIL.AC.UK
Emne: Re: [ccp4bb] Strategies for increasing Trp content of proteins

We have had success placing single trp on the outside of proteins, as weird as 
it sounds it works pretty well. If your protein is easy to express you can try 
a few choices.

If your protein is difficult to express, a fusion with a trp-positive domain or 
with gfp may be a better option.

There are many other options but their application is best considered with more 
information in hand

Artem

On Fri, Feb 18, 2022, 8:02 PM Tanner, John J. 
mailto:tanne...@missouri.edu>> wrote:

Dear CCP4BB,

We are working on a protein that has no Trp residues, which makes 
chromatography challenging due to the low absorbance at 280 nm (Abs 0.1% = 
0.104). Does anyone have experience using mutagenesis to increase the Trp 
content of proteins?

Thanks,

Jack Tanner

--
John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu<mailto:tanne...@missouri.edu>
https://cafnrfaculty.missouri.edu/tannerlab/
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A

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[ccp4bb] Strategies for increasing Trp content of proteins

2022-02-18 Thread Tanner, John J.

Dear CCP4BB,

We are working on a protein that has no Trp residues, which makes 
chromatography challenging due to the low absorbance at 280 nm (Abs 0.1% = 
0.104). Does anyone have experience using mutagenesis to increase the Trp 
content of proteins?

Thanks,

Jack Tanner

--
John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu<mailto:tanne...@missouri.edu>
https://cafnrfaculty.missouri.edu/tannerlab/
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A






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[ccp4bb] MizzouForward faculty hiring campaign

2021-11-17 Thread Tanner, John J.

Dear Colleagues:

The University of Missouri has initiated a major faculty hiring campaign, 
called MizzouForward, which intends to hire 150 new faculty members over the 
next 5 years.  Successful candidates must be research leaders with a passion 
for collaboration and a proven track record of active, external research 
funding, particularly from federal agencies like NIH. This initiative coincides 
with the recent grand opening of the NextGen Precision Health research 
building, which houses a newly upgraded imaging center with a Krios G4 and 
Aquilos Cryo-FIB. Other investments in structural biology include a share of 
ALS beamline 4.2.2 and a Bruker 800 MHz NMR with cryoprobe.  For more 
information, please see:

https://provost.missouri.edu/mizzou-forward/

--
Jack Tanner (tanne...@missouri.edu) and Lesa 
Beamer (beam...@missouri.edu)
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211






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Re: [ccp4bb] Looking for proteins for undergraduate biochemistry lab

2021-06-17 Thread Tanner, John J.

We developed a senior undergraduate biochemistry lab around an acid phosphatase 
from Francisella tularensis (FtHAP).

https://pubmed.ncbi.nlm.nih.gov/27980518/

The enzyme is easy to purify and crystallize, and the crystals diffract well. 
L-tartrate and phosphate ion are inexpensive inhibitors, which can be included 
in crystallization (3IT0/1). We have the students grow crystals and collect 
X-ray diffraction data remotely. Then they view maps in Coot. The enzyme assay 
is a simple colorimetric test with p-nitrophenylphosphate as the substrate.

--
John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu
https://cafnrfaculty.missouri.edu/tannerlab/
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A



From: CCP4 bulletin board  on behalf of P. H 

Date: Wednesday, June 16, 2021 at 5:19 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Looking for proteins for undergraduate biochemistry lab
WARNING: This message has originated from an External Source. This may be a 
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Hello All,

We are looking for some candidate proteins for an undergraduate level advanced 
biochemistry lab. They should be expressed in bacteria, simple enough to purify 
and it will be nice to perform some simple characterization experiments(binding 
assays, enzymatic assays).
Any suggestions?

Thank you in advance.
Prerna gupta



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[ccp4bb] Design of SUMO fusion proteins

2021-04-27 Thread Tanner, John J.

Sorry for the non-CCP4 question…

I would like ask your advice on designing SUMO fusion proteins. Specifically, 
is it recommended to include a linker between the C-terminus of SUMO (-QIGG) 
and the N-terminus of the target protein? Figure 3 of Guerrero et al. 
(https://pubmed.ncbi.nlm.nih.gov/26297996/) suggests that including a linker of 
SGG or SGGG greatly improves cleavage efficiency by Ulp1. However, the 
often-stated advantage of SUMO is that, in the absence of a linker, the target 
protein contains no extra residues after cleavage.

I’ll also take any advice on your favorite N-terminal His tag for SUMO fusions. 
I am considering MGSSHHG, based on two Acta F papers 
(https://pubmed.ncbi.nlm.nih.gov/22949189/, 
https://pubmed.ncbi.nlm.nih.gov/18391421/), or perhaps MGSSHHSSG, which is 
from pET14b.

Thanks,

Jack


--
John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu
https://cafnrfaculty.missouri.edu/tannerlab/
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A








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Re: [ccp4bb] unknown density

2021-03-22 Thread Tanner, John J.

Could be 5 water molecules. Pentagons of water molecules are common in high 
resolution structures. Add 5 waters and see if the inter-water distances are 
appropriate for hydrogen bonding  (2.5-3.2 A).

From: CCP4 bulletin board  on behalf of Sam Tang 

Date: Monday, March 22, 2021 at 9:00 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] unknown density
WARNING: This message has originated from an External Source. This may be a 
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Hello fellow colleagues

Hope you are all well while the pandemics persists. I just wonder if anyone may 
have an idea what this density (looking like a pentagon) might be. The data was 
collected to 1.8 A and crystal was grown in Bis-tris + PEG3350. Imidazole 
residual? Nucleotide (the protein itself is nucleotide-binding, but shouldn't 
be at this particular site)?

https://drive.google.com/file/d/1L9UBFmW72P214itM2HJR_DVy3FaA6FEZ/view?usp=sharing

Thanks!

BRS

Sam

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[ccp4bb] Tiny rocks on my CX100 shipping dewar

2020-12-04 Thread Tanner, John J.

When we opened our CX100 shipping dewar returned from APS via FedEx this week, 
we observed what appears to be tiny rocks on the rim below the foam neck core:

https://www.dropbox.com/s/ky09a1vbm9t0mrl/CX100withrocks.png?dl=0

Has anyone seen this before? Is this perhaps the absorbent material from the 
inside of the dewar?

Thanks,

Jack

John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu
https://cafnrfaculty.missouri.edu/tannerlab/
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A



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[ccp4bb] Tenure track faculty position University of Missouri

2020-10-07 Thread Tanner, John J.

Dear Colleagues,

My department has begun a search for a tenure track faculty position. 
Structural biology is among the preferred areas of biochemistry for this 
search. More information in available here:

https://biochem.missouri.edu/open-positions/

Review of applications will begin on November 16, 2020.

John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A




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Re: [ccp4bb] How to fix: residues with missing atoms

2020-05-23 Thread Tanner, John J.

Try SWISS-MODEL.

Sent from Jack's iPhone

On May 23, 2020, at 6:24 PM, Eugene Osipov  wrote:


Dear Yong,
you could use freely available Chimera.Use Tools->Structure Editing-> Dock 
prep. in order to add missing side chains to your protein.
Another option - Protein preparation tool from Schrodinger Suite. However, it 
is non-free.


сб, 23 мая 2020 г. в 21:19, Yong Tang 
mailto:liutan...@gmail.com>>:
Dear all, is there a way to "automatically" patch up the missing atoms in the 
residues that otherwise are properly defined in a PDB entry. For example, an 
Arginine is defined as Arginine but only has the beta carbon on the side chain.

In Coot I could use the Extensions/Modeling/Residues with Missing Atoms to 
identify these residues and then go down the list to "mutate" them one by one 
by hand. Is there anything more efficient? I could also use the 
Calculate/Mutate Residue Range but this inevitably changes the "good" residue 
side chains also.

Any tip is much appreciated, -yong



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--
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O



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Re: [ccp4bb] Covalent Cysteine Aduct

2020-03-27 Thread Tanner, John J.

It looks like the density suggests an S-S bond.  Perhaps try CME?

https://www.rcsb.org/ligand/CME


John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S. College Ave.
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-5635
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A






On Mar 27, 2020, at 3:32 PM, Cowan, Richard H. (Dr.) 
mailto:rc...@leicester.ac.uk>> wrote:

Hi All,

During the current enforced shutdown, I've been going back over some older data 
and spotted this in one of my structures:




It's what appears to be a covalent aduct onto a cysteine on the surface 
(originally modeled as 2 waters!). The condition was optimized from the 
Morpheus Screen condition D1, so MES/Imidazole pH 6.5, PEG 500MME, PEG20k and a 
mix of 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol, 2-Propanol, 1,4-Butanediol 
and 1,3-Propanediol. The data has been cut at 1.7A, with good stats.

Has anyone seen anything like this before? what do you think my best bet for 
modeling this is? and aduct of 1,3-propanediol? It looks too short for 
1-butanol or 1,4-butandiol, and it's linear so 2-propanol and 1,2-propanediol 
seem unlikely.

Thanks,

Dr Richard Cowan
Research Associate

HWLSB 1/05
Department of Biochemistry
University of Leicester
Lancaster Road
Leicester, LE1 9HN, U.K.

Phone +44 (0) 116 229 7077



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Re: [ccp4bb] Flexible C terminus

2020-03-12 Thread Tanner, John J.

Dear Chitra,

Try adding a ligand to the crystallization. This worked for us with ALDH7A1:

https://www.ncbi.nlm.nih.gov/pubmed/26260980

ALDH7A1 is an example of an enzyme with a flexible C-terminus (11 residues). 
The conformation of the C-terminus depends on the presence of a ligand in the 
substrate site. With the product bound, the C-terminus adopts the “in” 
conformation (4ZUL). Without the product bound, the C-terminus adopts either 
the “out” conformation (4ZUK, chains A-F,H) or is disordered (4ZUK, chain G).

In this case, the flexibility of the C-terminus is essential for catalytic 
activity:.

https://www.ncbi.nlm.nih.gov/pubmed/29045138

Good luck!

Jack

John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S. College Ave.
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-5635
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A






On Mar 12, 2020, at 8:01 AM, Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>> wrote:

Hi Chitra Latka,

By far the best approach is to find what protein is interacting with the one 
you have the structure and try co-crystallizing them together. At least there 
will be some more biology (science) involved in what you will be doing. You may 
get lucky and get different packing of your full length protein and get some 
sort of structure for last 20 aa. Then what?

Regards,

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of chitra latka
Sent: Thursday, March 12, 2020 3:54 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Flexible C terminus

Dear All,

I am working on a protein that has flexible C terminus. None of the available 
structures even in homologs have density for C term region (around 20 odd 
residues). All the available pdb entries have missing density for these 20 
residues at C terminus.

I am going to try my luck crystallising the entire protein in hope of getting 
density for C term residues as well (Fingers crossed).

Has anyone faced a similar problem where they have managed to get density for a 
flexible terminus successfully?

Any suggestions would be appreciated.

Cheers !

Chitra Latka




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Re: [ccp4bb] MD program suitable to compute trajectories of a very small molecule in a protein

2020-01-23 Thread Tanner, John J.

Fred,

You might want to review the literature on using MD to study diffusion of O2/CO 
in myoglobin.

Jack

John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A

On Jan 23, 2020, at 3:43 AM, Fred Vellieux 
mailto:frederic.velli...@lf1.cuni.cz>> wrote:

Dear all,

I need to run MD calculations in order to follow the trajectories of a very 
small molecule inside a protein. From previous calculations (not MD) I have 
starting positions for this small molecule that all seem in agreement with a 
possible path of motion inside the protein.

Now I need to access a MD program (without licensing costs).

I've had a look at the software list provided in Wikipedia (and tried to 
install the software, in succession, alas without success):

cp2k - present for CentOS6 (with yum install ?) but appears to have vanished 
for CentOS7;

gromacs requires a gcc version I don't have (even after having compiled and 
installed a suitable gcc version, cmake complains about the "old version" and 
stops);

NWChem is unhappy with the Python setup and doesn't compile.

I don't know how to solve all these OS version, library, unsuitable binary etc 
problems. In fact I don't know if any of these 3 software suites would be 
suitable for what I have in mind.

Hence would anyone know of a useful MD software suite that would be suitable 
for my purpose and comes with statically linked binaries suitable for Intel 64 
(Linux) ? Just launch the executable and it runs, no questions asked...

Thank you,

Fred.



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Re: [ccp4bb] Unusual monomer-monomer interface in crystal

2020-01-21 Thread Tanner, John J.

Chris,

We observed electron density for an intermolecular disulfide bond in a protein 
that appears to be monomeric in solution.

See Cys166 in 4DSG or 4DSH.

https://www.ncbi.nlm.nih.gov/pubmed/22646091

Jack

John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A

On Jan 21, 2020, at 11:55 AM, Chris Fage 
mailto:fage...@gmail.com>> wrote:

Dear CCP4BB Users,

I've recently solved the ~2.2 angstrom structure of a protein. In my electron 
density there are unusual monomer-monomer interfaces involving pairs of His and 
Cys residues (see https://ibb.co/wdWBcdk). Note the positive Fo-Fc density 
between the four side chains. As there is not adequate space for a water 
molecule or metal ion, perhaps the Cys residues are partially tied up disulfide 
bonds? However, the protein looks to be fully monomeric based on LC-MS 
measurements. Has anyone else observed crystal-driven formation of disulfide 
bridges?

Aside from this region, there is no extensive interface between momoners, and 
PDBePISA suggests a monomeric state.

Thanks in advance for any advice!

Best wishes,
Chris



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Re: [ccp4bb] difficult molecular replacement solution

2019-11-13 Thread Tanner, John J.

Dear Rob,

Based on our experience with difficult MR cases, I recommend performing 
refinement on the coordinates from MR (I prefer PHENIX simulated annealing for 
this step). Then send the refined map - WITHOUT the model - to automated 
building with density modification. The auto-built model may give you an 
indication of how many chains are in the asymmetric unit. You could do this 
procedure for each of the MR solutions (N=4,5,6) and compare the results. Also, 
if you enable automatic detection of NCS during DM, you may find that 6 NCS 
operators are found even when N=4 or 5; this would give you confidence that N=6 
is possible.

Also look at the cross rotation function to see how many strong peaks are 
present. I’m sure the peaks are listed in Phaser, but it is easier for me to 
find them in the MOLREP output.  MOLREP also provides a matrix that tells you 
which cross RF peaks are related by symmetry and which are unique, which is 
helpful.

And David Schuller mentioned inspecting the self-RF, which is a good idea.

Finally, do you know anything about the oligomeric state of the protein? If it 
is a pentamer, N=6 seems unlikely. If it is a dimer, N=5 in P212121 seems 
unlikely.

Jack

John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A

On Nov 13, 2019, at 8:33 AM, Robert S Phillips 
mailto:p...@uga.edu>> wrote:

I have been working on a protein structure which has been hard to solve by 
molecular replacement.

Unit cell: (60.6, 172.34, 196.42, 90, 90, 90)
Space group: P 21 21 21

The problem is that the homologues have only ~20% identity, and there are 
multiple chains in the asymmetric unit.  The question is how many.  It could be 
4, 5, or 6 chains.

N  solvent   P
 4  0.602   3.090.225
 5  0.502   2.470.388
 6  0.403   2.060.229

I have run PHASER with 4, 5 and 6 chains.  I allowed it to search all possible 
space groups, and P212121 was the best solution.  These are the results.

N  LLG   TFZ
4  104.97.5
5  137.57.7
6  166.28.3

 Am I correct to conclude that there are 6 chains in the asymmetric unit?

Rob

Robert S. Phillips
Professor of Chemistry and of Biochemistry and Molecular Biology
University of Georgia
Athens, GA 30602
Phone: (706) 542-1996
Fax: (706) 542-9454
E-mail: rsphill...@chem.uga.edu
Web:  
http://tryptophan.net


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[ccp4bb] Two tenure-track faculty openings at Univ. of Missouri Biochemistry

2019-10-14 Thread Tanner, John J.

Dear Colleagues,

My department has two tenure-track faculty openings.

Review of applications will begin on November 15, 2019.

Click the link below for more information.

https://biochem.missouri.edu/open-positions/

John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A




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Re: [ccp4bb] Changes in quaternary structure

2019-10-09 Thread Tanner, John J.

The same enzyme adopting different quaternary structures is a form of 
allosteric regulation. Jaffe's group has described this phenomenon - the 
“morpheein" model of allosteric regulation.

Reviews:
https://www.ncbi.nlm.nih.gov/pubmed/22182754
https://www.ncbi.nlm.nih.gov/pubmed/16023348



John J. Tanner, PhD
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S. College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html





On Oct 9, 2019, at 6:14 AM, Gabriela GARCIA RODRIGUEZ 
mailto:gabriela.garcia.rodrig...@vub.be>> 
wrote:

Dear CCP4BB subscribers,

I am writing a discussion on extensive quaternary changes between two different 
homodimers of the same protein and I would like to ask you for any examples of 
your own work/that you know of to include in my analysis. Basically, any 
proteins known to exist in two different (or more) homodimerised states 
(suffering changes in domain organisation between states would be even more 
interesting).
I would greatly appreciate any examples! Thank you for your time and attention.

Warm regards,

Gabriela


Gabriela Garcia Rodriguez

gabriela.garcia.rodrig...@vub.be

PhD candidate

Structural Biology Research Centre (SBRC)

Vlaams Instituut voor Biotechnologie (VIB) - Vrije Universiteit Brussel (VUB)

Pleinlaan 2- 1050 Brussels, Belgium








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Re: [ccp4bb] COOT crashes when I merge molecules

2019-06-10 Thread Tanner, John J.

Merging EDO into a structure also crashes in Coot 0.8.9.2 running on linux.


John J. Tanner
Professor of Biochemistry and Chemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A

On Jun 10, 2019, at 1:53 PM, Franz St John 
mailto:fjstj...@gmail.com>> wrote:

I'm having a similar issue with the same Coot version in both Ubuntu 18.04.2 
LTS and Win 10 (WinCoot). Merging an added water crashes while an added K or 
PO4 does not.



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[ccp4bb] Chair of the Department of Molecular Microbiology and Immunology at Univ. of Missouri

2018-06-18 Thread Tanner, John J.

The Department of Molecular Microbiology and Immunology at the University of 
Missouri is searching for a new Chair. Please see the links below for 
information about the department and the position. I would be happy to discuss 
this opportunity offline with interested people.

https://medicine.missouri.edu/departments/molecular-microbiology-immunology

https://medicine.missouri.edu/sites/default/files/MMI_Chair_Advertisement-APPROVED.pdf

John J. Tanner
Professor of Biochemistry and Chemistry
Interim Chair of Biochemistry
University of Missouri-Columbia
117 Schweitzer Hall
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-5635
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A





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Re: [ccp4bb] crysol or FoxS integration into python and pymol

2018-06-06 Thread Tanner, John J.

Dhiraj,

Download the  command line version of foxs from 
https://modbase.compbio.ucsf.edu/foxs/.

You can integrate foxs into linux scripts:

[tannerjj@dizzy ambiguity]$ cat FoXS.sh
#!/bin/bash
date
while read pdb
do
  echo "processing " $pdb
  /titan/tanner/SAXS/FoXS/foxs --max_q=0.32 $pdb $dat
done < filelist
date

You can also use wildcards: foxs *.pdb *.dat

Type foxs without arguments to get help:

[tannerjj@dizzy ~]$ foxs
/titan/tanner/SAXS/FoXS/foxs
Usage:   ...   ... :

Options:
  --helpAny number of input PDBs and profiles is
supported. Each PDB will be fitted against
each profile.
  --version FoXS (IMP applications)
Copyright 2007-2016 IMP Inventors.
All rights reserved.
License: GNU LGPL version 2.1 or later
.
Written by Dina Schneidman.
  -s [ --profile_size ] arg (=500)  number of points in the profile
  -q [ --max_q ] arg (=0.50)max q value
  --min_c1 arg (=0.99)  min c1 value
  --max_c1 arg (=1.05)  max c1 value
  --min_c2 arg (=-2.00) min c2 value
  --max_c2 arg (=4.00)  max c2 value
  -h [ --hydrogens ]explicitly consider hydrogens in PDB files
(default = false)
  -r [ --residues ] fast coarse grained calculation using CA
atoms only (default = false)
  -b [ --background_q ] arg (=0)background adjustment, not used by default.
if enabled, recommended q value is 0.2
  -o [ --offset ]   use offset in fitting (default = false)
  -p [ --write-partial-profile ]write partial profile file (default = false
)
  -m [ --multi-model-pdb ] arg (=1) 1 - read the first MODEL only (default), 2
- read each MODEL into a separate structure
, 3 - read all models into a single structu
re
  -v [ --volatility_ratio ] calculate volatility ratio score (default =
false)
  -l [ --score_log ]use log(intensity) in fitting and scoring
(default = false)
  -g [ --gnuplot_script ]   print gnuplot script for gnuplot viewing
(default = false)




On Jun 6, 2018, at 1:25 AM, Srivastava, Dhiraj 
mailto:dhiraj-srivast...@uiowa.edu>> wrote:

Hi All
 sorry for asking non-crystallography related question. Is it possible 
to integrate crysol or FoxS in python and pymol? I have generated thousands of 
models of my protein that I want to test against SAXS and other biochemical 
data. The ability to integrate the comparison of experimental and calculated 
X-ray scattering profile into python and pymol will be really helpful as I can 
easily calculate other parameter of my protein in pymol and compare it to other 
biochemical data. There is a pymol plugin available for SAXS but its not 
helpful for me as its not practical to use plugins for so many different 
models. I am looking for script that can automate the calculation.
 if anyone has script that can do this and is willing to share with 
me, that will be really helpful.

thank you
Dhiraj


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John J. Tanner, PhD
Professor of Biochemistry and Chemistry
Interim Chair, Department of Biochemistry
University of Missouri-Columbia
117 Schweitzer Hall
503 S. College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-2754
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html







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Re: [ccp4bb] covalent bond

2017-12-07 Thread Tanner, John J.

You can add a covalent bond by modifying this part of the PHENIX .def file via 
the gui:

  geometry_restraints.edits {
excessive_bond_distance_limit = 10
bond {
  action = *add delete change
  atom_selection_1 = None
  atom_selection_2 = None
  symmetry_operation = None
  distance_ideal = None
  sigma = None
  slack = None
}

John J. Tanner
Professor of Biochemistry and Chemistry
Chair, Biochemistry Department Graduate Admissions Committee
Department of Biochemistry
University of Missouri-Columbia
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-5635
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A

On Dec 7, 2017, at 11:40 AM, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Is that format correct?
Eleanor

On 7 December 2017 at 17:32, gerardo andres 
<130afa955101-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Hi everyone. I´m trying to make a covalent bond between a cystein residue of a 
protein and its ligand, but always that I do the refinement by Phenix, the 
ligand is placed outside of its electronic density. I edited the PDB file like 
this:
LINK SG  CYS A 215 C02 LIG C   1 , but this is not 
working.  Someone has some idea to address this problem?

Thanks,

Gerardo

Re: [ccp4bb] A challenging Molecular replacement

2017-07-17 Thread Tanner, John J.

Richard,

I can’t help you with 5XQL.

However, I can point out a recent structure from my group that might be useful 
for teaching. The structure was solved by MR with a search model that had 33% 
sequence identity and represented only 46% of the target structure. The Methods 
section of the paper has a detailed description of the phasing procedure. We 
used BALBES, then did autobuilding in phenix from the BALBES/REFMAC map.

https://www.ncbi.nlm.nih.gov/pubmed/28420730

John J. Tanner
Professor of Biochemistry and Chemistry
Chair, Biochemistry Department Graduate Admissions Committee
Department of Biochemistry
University of Missouri-Columbia
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-5635
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A

On Jul 17, 2017, at 11:01 AM, CDaddy 
<2295867...@qq.com> wrote:

I am a structural biologist who is teaching X-ray crystallography. Recently I 
noticed that BrlR structure (5XQL) was solved using molecular replacement with 
a search model of very low similarity. I am very interested in this structure 
because I think this a very good example to show students how to solve phase 
problem using molecular replacement, especially when the model and the target 
protein share a low sequence identity. However, when I downloaded the data from 
PDB, I found that I cannot solve the phase problem using Phaser as mentioned by 
the authors. During this procedure BmrR (PDB:1R8E) was used as the search 
model. I tried to consult the authors for help but receive no response by now. 
Since the description of this issue in the literature is very brief, could 
anyone please spend a little time on this molecular replacement and give me 
some advices on this issue? I like to learn some valuable tricks. Your 
assistance will be highly appreciated.

All the best,

Richard.

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Tanner, John J.

Relevant to this discussion, the 2018 ACA meeting in Toronto will have a 
session on

"Best practices for building, refining, and analyzing ligands in macromolecular 
structures”

co-chaired by Anna Gardberg and Kurt Krause.

I expect this session will include case studies of structures that went wrong 
as a way of educating the community about the potential pitfalls of building 
ligands into electron density.


John J. Tanner
Professor of Biochemistry and Chemistry
Chair, Biochemistry Department Graduate Admissions Committee
Department of Biochemistry
University of Missouri-Columbia
117 Schweitzer Hall
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-5635
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A



On Jun 27, 2017, at 1:34 AM, Trevor Sewell 
> wrote:


I have come across a key paper in my field that describes an enzyme mechanism. 
Their work is based on a deposited structure – by other authors - that is 
incorrectly interpreted.

Is there a process for removing a demonstrably wrong structure (deposited by 
others) from the PDB and replacing it with a correctly interpreted structure 
based on the original data? Or is there an alternative, and generally 
recognized, way of getting the correct structure in the public domain?

Many thanks for your advice on this matter.

Trevor Sewell

Disclaimer - University of Cape Town This e-mail is subject to UCT policies and 
e-mail disclaimer published on our website at 
http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 
650 9111. If this e-mail is not related to the business of UCT, it is sent by 
the sender in an individual capacity. Please report security incidents or abuse 
via cs...@uct.ac.za

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Tanner, John J.

Trevor,

I can share our recent experience correcting the record about a misplaced
ligand binding site. It represents one possible way to deal with erroneous
structures.

Our analysis of structures of the proline biosynthetic enzyme PYCR1 deposited
by another group in 2006 suggested that the NAD(P)H cofactor had been
erroneously modeled into noise density, placing the ligand over 25 Angstrom
from the canonical binding site for Rossmann fold enzymes. Because of our
longstanding interest in proline metabolism, I felt compelled to set the record
straight. Therefore, we generated a clone, purified the protein, and
determined several structures with different ligands bound. Sure enough, the
ligands in the 2006 structures were incorrect. The supplement to our paper
includes a thorough analysis of the electron density of the incorrect
structures (EDS maps, PDBREDO, and omit maps). We also did kinetics and
analytical ultracentrifugation studies. In short, we did a fairly
comprehensive biochemical and biophysical study of the enzyme. Thus, pointing
out someone else’s error was just one part of a larger paper.

http://faculty.missouri.edu/%7Etannerjj/tannergroup/pdfs/PYCR1JBC2017withSupp.pdf<http://faculty.missouri.edu/~tannerjj/tannergroup/pdfs/PYCR1JBC2017withSupp.pdf>

https://www.ncbi.nlm.nih.gov/pubmed/28258219

Jack Tanner

John J. Tanner
Professor of Biochemistry and Chemistry
Chair, Biochemistry Department Graduate Admissions Committee
Department of Biochemistry
University of Missouri-Columbia
117 Schweitzer Hall
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-5635
Email: tanne...@missouri.edu<mailto:tanne...@missouri.edu>
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A

On Jun 27, 2017, at 1:34 AM, Trevor Sewell
<trevor.sew...@uct.ac.za<mailto:trevor.sew...@uct.ac.za>> wrote:

I have come across a key paper in my field that describes an enzyme mechanism.
Their work is based on a deposited structure – by other authors - that is
incorrectly interpreted.

Is there a process for removing a demonstrably wrong structure (deposited by
others) from the PDB and replacing it with a correctly interpreted structure
based on the original data? Or is there an alternative, and generally
recognized, way of getting the correct structure in the public domain?

Many thanks for your advice on this matter.

Trevor Sewell

Disclaimer - University of Cape Town This e-mail is subject to UCT policies and
e-mail disclaimer published on our website at
http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21
650 9111. If this e-mail is not related to the business of UCT, it is sent by
the sender in an individual capacity. Please report security incidents or abuse
via cs...@uct.ac.za<mailto:cs...@uct.ac.za>

Re: [ccp4bb] Incorrect Structure in the PDB

2017-06-27 Thread Tanner, John J.

Trevor,

I can share our recent experience correcting the record about a misplaced
ligand binding site. It represents one possible way to deal with erroneous
structures.

http://faculty.missouri.edu/%7Etannerjj/tannergroup/pdfs/PYCR1JBC2017withSupp.pdf<http://faculty.missouri.edu/~tannerjj/tannergroup/pdfs/PYCR1JBC2017withSupp.pdf>

https://www.ncbi.nlm.nih.gov/pubmed/28258219

Jack Tanner

On Jun 27, 2017, at 1:34 AM, Trevor Sewell
<trevor.sew...@uct.ac.za<mailto:trevor.sew...@uct.ac.za>> wrote:

I have come across a key paper in my field that describes an enzyme mechanism.
Their work is based on a deposited structure – by other authors - that is
incorrectly interpreted.

Many thanks for your advice on this matter.

Trevor Sewell

Re: [ccp4bb] NAD dihedral for C2N-C3N-C7N-N7N

2017-05-17 Thread Tanner, John J.

I’m not aware of a wide study on NAD carboxamide conformation. Lacking atomic 
resolution, optimizing the hydrogen bonding can be used to determine the 
orientation of the carboxamide, as you wrote. You may have to consider 
intramolecular hydrogen bonding within NAD+ as well as intermolecular hydrogen 
bonding with the protein. For example, Fig. 5 from below shows a case in which 
the carboxamide of NADPH donates a hydrogen bond to a backbone carbonyl, while 
accepting a hydrogen bond from the NADPH pyrophosphate.

https://www.ncbi.nlm.nih.gov/pubmed/28258219


John J. Tanner
Professor of Biochemistry and Chemistry
Chair, Biochemistry Department Graduate Admissions Committee
Department of Biochemistry
University of Missouri-Columbia
117 Schweitzer Hall
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-5635
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A



On May 17, 2017, at 2:46 PM, Jorge Iulek 
> wrote:

Dear all,

I came across some difficulty to refine a NAD molecule in a structure, 
specially its amide of the nicotinamide moiety.
A (very) brief search in deposited structures seems to point that not so 
ever the C2N-C3N-C7N-N7N dihedral is close to either 0 or 180 degrees, but in 
most cases it is to one of these, with a preference towards 0 degrees. Another 
search in the literature, and I could not find any study on either NAD or even 
the nicotinamide alone to calculate the energy barrier to rotate around this 
bond (in vacuum, eg).
My data quality and resolution do not put much confidence on B-factor 
differences, but they seem to indicate that the cited dihedral angle should be 
close to 180 degrees, id est, O7N is "closer" to C2N (and, consequently, to 
N1N) than N7N is. In fact, I have a glutamine nearby whose terminal amide is 
interacting with the nicotinamide amide, so my idea is to make one's nitrogen 
to interact with other's oxygen. Concerning b-factor differences for this 
glutamine, they favor its NE2 to point to nicotinamide amide, what would imply 
that the C2N-C3N-C7N-N7N dihedral to would be close to 180 degrees rather than 
0 degree.
Is there any wide study on NAD nicotinamide amide conformation? Specially, 
bound to protein structures?
Thanks,

Jorge

Re: [ccp4bb] Structure comparison

2017-04-10 Thread Tanner, John J.

TM-align is used in the protein structure prediction community.

-Jack Tanner

Sent from Jack's iPhone

> On Apr 10, 2017, at 8:45 PM, Goldman, Adrian  
> wrote:
> 
> The right people to look at for this are found in the structure prediction 
> community; a series of algorithms were developed to compare different 
> predictions of the same structure.  Look for papers from about CASP-3 (John 
> Mount) or pick up any recent CASP and look at how they compare the different 
> predictions and follow the literature back.
> 
> Adrian
> 
> 
>> On 10 Apr 2017, at 00:44, Gert Vriend  wrote:
>> 
>> Arthur Lesk (at Penn state Univ, I think)m is the only one I know who has 
>> worked on this topic. I suggest you ask him. The topic you elude to is 
>> commonly known as the Russian Doll Effect.
>> 
>> If you want to discuss the topic, feel free to Skype me.
>> 
>> Greetings
>> 
>> Gert Vriend
>> 
>> 
>>> On 10-4-2017 1:37, Reza Khayat wrote:
>>> Hi,
>>> 
>>> My initial e-mail may have been a bit vague so I'll try to be more 
>>> specific. Superposing the structures and comparing them against one 
>>> another, while appropriate, is a subjective way to do the analysis as I 
>>> would have to subjectively define a threshold that would indicate a 
>>> difference between the structures. My threshold may be grossly different 
>>> than someone else's threshold. I am interested in an objective criterion. 
>>> One where strong emphasis has been put on error analysis and error modeling 
>>> in terms of both the refined structure and the underlying data. I realize 
>>> that defining such criterion is by no means trivial. Thanks again for the 
>>> help.
>>> 
>>> Best wishes,
>>> Reza
>>> 
>>> Reza Khayat, PhD
>>> Assistant Professor
>>> City College of New York
>>> Department of Chemistry
>>> New York, NY 10031
>>> 
>>> 
>>> From: Reza Khayat
>>> Sent: Sunday, April 9, 2017 6:07 PM
>>> To: CCP4 bulletin board
>>> Subject: Structure comparison
>>> 
>>> Hi,
>>> 
>>> I have refined several structures of a protein from different space groups 
>>> and would like to compare them to one another. Is there a program/software 
>>> suite that would provide an objective comparison of the structures and 
>>> identify regions where the structures are sufficiently different from one 
>>> another to warrant a closer look? I think the most important aspect of the 
>>> analysis would be defining a threshold (possibly based on resolution and 
>>> structure statistics) that would identify sufficient difference between 
>>> structures. Thanks.
>>> 
>>> Best wishes,
>>> Reza
>>> 
>>> Reza Khayat, PhD
>>> Assistant Professor
>>> City College of New York
>>> Department of Chemistry
>>> New York, NY 10031

[ccp4bb] Request for session proposals for ACA Toronto 2018

2017-02-13 Thread Tanner, John J.

Colleagues,

My apologies for sending this message to CCP4BB, but I wanted to make sure to 
reach as many BioMac SIG members and other potential attendees as possible.


The Biological Macromolecules Scientific Interest Group (BioMac) of the 
American Crystallographic Association requests your input for planning the 
scientific sessions to be held at the ACA National Meeting in Toronto on July 
20-24, 2018.

The procedure for planning the BioMac program at ACA 2018 has 5 phases:

Phase 1. BioMac SIG members (or other interested colleagues in the field) 
propose sessions (see below).
Phase 2. BioMac SIG officers review proposals for thematic overlap and work 
with the proposers to combine session ideas where possible and identify 
co-sponsoring SIGS.
Phase 3. The proposals are made available for review by the BioMac SIG members.
Phase 4. BioMac SIG members prioritize the sessions by voting at the SIG 
meeting at the 2017 New Orleans meeting.
Phase 5. SIG officers convey the results to the ACA during the planning session 
held after the 2017 New Orleans meeting.

We are in Phase 1. If you want to propose a session, fill out the word document 
linked below, including the session title, session chairs and their 
affiliations, description of the theme, and potential speakers. Email the 
document to me (use reply keeping the subject line, not reply-all). Deadline 
for submitting proposals is March 1, 2017.

We look forward to your input.

Sincerely,

Jack Tanner
Chair BioMac SIG

Session proposal form:

https://www.dropbox.com/s/lwgtu08g2oy9lyc/TorontoSessionProposal.docx?dl=0
https://www.dropbox.com/s/8p1yce872vkcje5/TorontoSessionProposal.pdf?dl=0

Re: [ccp4bb] RMSD plot

2017-02-01 Thread Tanner, John J.

CNS, if sequences are identical.


Sent from Jack's iPhone

> On Feb 1, 2017, at 4:26 AM, Madhuranayaki Thulasingam  
> wrote:
> 
> Dear all,
> 
> I would like to plot RMSD vs amino acids for two superimposed crystal 
> structures.
> 
> Can anyone suggest me a way to do it.
> 
> Thanks in advance,
> Madhu.

Re: [ccp4bb] For stabilizing protein-protein complex

2017-01-31 Thread Tanner, John J.

If your goal is a crystal structure, this reference may be worth consulting.  
The paper describes the use of centrifugal concentrators to make a complex of 
two proteins that have Kd of 19 micromolar for crystallization.  They mixed the 
two proteins and then concentrated using a membrane that allows passage of the 
smaller protein while retaining the complex.  The protein-protein complex 
crystallized.

Ignatev A, Piatkov K, Pylypenko O, Rak A. A size filtration approach to purify
low affinity complexes for crystallization. J Struct Biol. 2007 
Jul;159(1):154-7.
PubMed PMID: 17408969.


John J. Tanner
Professor of Biochemistry and Chemistry
Chair, Biochemistry Department Graduate Admissions Committee
Department of Biochemistry
University of Missouri-Columbia
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-5635
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A

On Jan 31, 2017, at 10:05 AM, sanjeev kumar 
>
 wrote:

Dear all,

I am trying to stabilize a protein-protein complex. Our SPR study indicates it 
is having micro molar dissociation constant. I tried to purify both the 
molecule in complex form with size exclusion chromatography (mixed both the 
protein in equal molar ratio and incubated at 4 degree for 1 hour), I didnt 
observed formation of complex as both the molecule eluted at their respected 
elution volume.
Please suggest me to get a better way to achieve the complex and if anyone 
gives idea about what is the good cross-linker I can use.
Suggestions are highly appreciated.

Thanks

best
sanjeev kumar, PhD
Purdue University
West Lafayette
Indiana

Re: [ccp4bb] handling crystals in volatile solvents

2015-06-12 Thread Tanner, John J.

This paper might be helpful.

1. J Struct Biol. 2014 Nov;188(2):102-6. doi: 10.1016/j.jsb.2014.09.011. Epub 
2014
Oct 5.

Efficient cryoprotection of macromolecular crystals using vapor diffusion of
volatile alcohols.

Farley C, Juers DH.

Author information:
(1)Department of Physics, Whitman College, Walla Walla, WA 99362, United States.
(2)Department of Physics, Whitman College, Walla Walla, WA 99362, United States;
Program in Biochemistry, Biophysics and Molecular Biology, Whitman College, 
Walla
Walla, WA 99362, United States. Electronic address: 
juer...@whitman.edumailto:juer...@whitman.edu.

Macromolecular X-ray crystallography, usually done at cryogenic temperature to
limit radiation damage, often requires liquid cryoprotective soaking that can be
labor intensive and damaging to crystals. Here we describe a method for
cryoprotection that uses vapor diffusion of volatile cryoprotective agents into
loop-mounted crystals. The crystal is mounted into a vial containing a small
volume of an alcohol-based cryosolution. After a short incubation with the 
looped
crystal sitting in the cryosolution vapor, the crystal is transferred directly
from the vial into the cooling medium. Effective for several different protein
crystals, the approach obviates the need for liquid soaking and opens up a
heretofore underutilized class of cryoprotective agents for macromolecular
crystallography.

PMCID: PMC4252874 [Available on 2015-11-01]
PMID: 25286441  [PubMed - in process]

John J. Tanner
Professor of Biochemistry and Chemistry
Chair, Biochemistry Department Graduate Admissions Committee
University of Missouri-Columbia
125 Chemistry Building
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-2754
Email: tanne...@missouri.edumailto:tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html

On Jun 12, 2015, at 4:11 PM, Thomas, Leonard M. 
lmtho...@ou.edumailto:lmtho...@ou.edu
 wrote:

Hi All,

We have gotten some very nicely formed crystals out of a couple of different 
volatile solvents recently.  Besides looking for something easier to work in 
does anybody have any tips on handling crystals from these types of solvents.  
It is very hard to loop a crystal while it is doing the backstroke in the well 
with all of its buddies.

Thanks in advance.
Len

Leonard M. Thomas Ph.D.
Macromolecular Crystallography Laboratory Manager
University of Oklahoma
Department of Chemistry and Biochemistry
Stephenson Life Sciences Research Center
101 Stephenson Parkway
Norman, OK 73019
405-325-1126
lmtho...@ou.edumailto:lmtho...@ou.edu
http://barlywine.chem.ou.edu
http://structuralbiology.ou.edu

Re: [ccp4bb] Off topic - modeling multi-domain protein

2015-05-12 Thread Tanner, John J.

This seems like a good problem for SAXS rigid body modeling.  We previously 
used an approach based on docking models into SAXS envelopes with the 
constraint of 2-fold symmetry, followed  by scoring the dimer  models using the 
goodness of fit to the experimental curve (1).  Another approach would be to 
use CORAL, which we have used to model a multi domain monomer (2).  CORAL 
allows the enforcement of symmetry for oligomers.  Either way, you can use 
target decoy analysis to get an idea of the confidence in the models (2).  In 
your case knowing the quaternary structure of the N-terminal domains provides a 
powerful constraint for SAXS modeling.

(1) http://www.ncbi.nlm.nih.gov/pubmed/22013066
(2) http://www.ncbi.nlm.nih.gov/pubmed/25137435

Jack Tanner

Sent from Jack's iPad

On May 12, 2015, at 12:56 AM, Victor Xiao 
victor41...@gmail.commailto:victor41...@gmail.com wrote:

Dear all,

I am trying to model a full-length double-domain protein in dimer. The 
structure of both N and C terminal domains are known and the linker region of 5 
residues are present in both structure (the linker might be flexible though). 
The N-terminal domain's structure is also a dimer, which can be used as another 
restraint.

Does anyone know any good tool for modeling such full-length dimer? Thanks in 
advance.

Best,

Xiao

Re: [ccp4bb] Thin plate crystals

2015-04-24 Thread Tanner, John J.

Following up on Dave's suggestion, you could try using crystal screens as 
additives.  This has worked well in my lab. The idea is to mix the condition 
that you currently have (the base) with all the crystal screen reagents you 
have in stock (CS, Index, etc.).  As a first trial, use reservoirs containing 3 
parts base and 1 part screen.  This generates a new matrix of hits.  You might 
find a condition that produces thicker crystals or perhaps a new new crystal 
form. I think this approach is described in the literature but don't remember 
the citation.

Jack



On Apr 24, 2015, at 12:31 AM, David Briggs wrote:


Hi,

In my experience, additive screens (e.g Hampton's) can change crystal 
morphology. You could also re-screen for new conditions either using matrix 
micro seeding, or change the protein buffer. Perhaps adding a ligand or a 
component from your current crystallisation conditions to your protein stock?

HTH,

Dave

On Fri, 24 Apr 2015 04:02 Prerana G. 
tracy...@gmail.commailto:tracy...@gmail.com wrote:
Dear all,

I am working on a protein (40kDa) which forms very thin plate shaped crystals 
which diffracts at very low resolution. Protein concentration that i have used 
for crystallisation is approx. 8mg/ml. I have attached the picture of the 
protein crystal.


How can I improve upon the shape of the crystal?



John J. Tanner, PhD
Professor of Biochemistry and Director of Graduate Admissions and Recruitment
Professor of Chemistry (Joint Appointment)
University of Missouri-Columbia
125 Chemistry Building
Columbia, MO  65211
email: tanne...@missouri.edumailto:tanne...@missouri.edu
phone: 573-884-1280
fax: 573-882-2754
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html

Re: [ccp4bb] clarification Re: Density fit analysis in Coot, and FEM

2015-02-22 Thread Tanner, John J.

Hi Emily,

It could be a scaling issue. Coot has a parameter under
Extensions...Refine...Set Density Fit Graph Weight... Making this value
smaller will make the bars shorter and greener. So if the two maps (or
coefficients) are on different scales, you will need different values of the
Set Density Fit Graph Weight to make the two sets look similar.

Jack

On Feb 20, 2015, at 9:11 AM, Emilia C. Arturo (Emily) wrote:

Thank you for the multiple kind off-list responses I received regarding how to
interpret map colors in Coot. I'm very grateful for the references, but it
seems that I did not state my issue clearly :-) What I was referring to was the
tool that Coot has under Validate Density Fit analysis. The tool outputs
graphs like the ones I'm pasting below. Both sets of graphs were generated from
the same pdb file, but the very-red bar graphs were calculated using the map
coefficients phenix had generated along with this model, while the mostly green
bar graphs pasted separately below, showing bars for the same stretch of
residues in each chain, were generated using the feature enhanced map that
phenix generated from this same model.Screen Shot 2015-02-20 at 9.56.22
AM.pngScreen Shot 2015-02-20 at 9.56.49 AM.png How do I interpret the fact
that the FEM and 2Fo-Fc maps give such different fits for the same model using
this type of analysis? ...or are the fits really that different (and maybe
green versus red is not as big as the visual cue would have me assume)?

Emily.

On Thu, Feb 19, 2015 at 11:00 AM, Emilia C. Arturo (Emily)
ec...@drexel.edumailto:ec...@drexel.edu wrote:
Hello all.
I'd like to understand what it is I'm looking at when I use Coot's density fit
analysis tool. I recognize that there was a post related to this topic on the
Coot bb a while ago --the discussion was on how to interpret the red-ness or
green-ness of the density fit plot
(https://www.mail-archive.com/coot@jiscmail.ac.uk/msg02995.html)https://www.mail-archive.com/coot@jiscmail.ac.uk/msg02995.html)--but
--but it doesn't seem the issue was resolved then (i.e. what does 'red' really
mean? is it ...bad?). Now I have more to ask that involves my using
phenix-generated FEMs to build in Coot.

So what I've done is the following: I adjust my model in Coot, using a
phenix-generated FEM as the map for fitting, then refine with phenix, and using
the refined pdb and reflections file, I use phenix to generate a new FEM. Then
I repeat. At some point I learned about Coot's density fit analysis tool and
took a look at how my model fits. If the map that is selected in the sidebar of
Coot is a FEM, then the density fit analysis plot looks mostly green everywhere
- fine. If, however, I select as my map in the Coot sidebar the 2Fo-Fc that
phenix had generated along with the latest refined model--the one I'm examining
with the density fit analysis tool--then Coot's density fit analysis plot looks
red (with values ~ 0.3), with splashes of orange, barely any green or yellow
(with values ~ 0.3), almost everywhere.

So these are my questions: What are the units of the density fit values? i.e.
What is the calculation that's done? I'm surprised that the FEM-dependent
density fit graphs look so different (i.e. so green) relative to the graphs
generated if my map is set to the 2Fo-Fc from the loaded model; both maps came
from the same model. In fact, I got worried, but then I realized that I don't
actually understand the red-ness and green-ness. I'm quite new to the business
of crystallography so any input is welcome regarding the use of FEMs and
density fit analyses.

Emily.
Ph.D. program in Biochemistry, Drexel Univ. College of Medicine
Jaffe lab, Fox Chase Cancer Center
Philadelphia, PA

Re: [ccp4bb] asymmetric homotrimer in the asu

2014-12-12 Thread Tanner, John J.

Two thoughts on asymmetric oligomers.

1. Here is a recent survey of asymmetric homodimers in the PDB. I know you
are looking for trimers, but at least this provides a precedent for asymmetric
oligomers.

Swapna LS, Srikeerthana K, Srinivasan N. Extent of structural asymmetry in
homodimeric proteins: prevalence and relevance. PLoS One. 2012;7(5):e36688. doi:
10.1371/journal.pone.0036688. Epub 2012 May 22. PubMed PMID: 22629324; PubMed
Central PMCID: PMC3358323.

2. SAXS is a very effective method for determining whether assemblies observed
in crystals are stable in solution, since it provides not only the oligomeric
state, but also the quaternary structure. The oligomeric state can be obtained
from the volume of correlation (1) and Porod-Debye analysis (2). The
quaternary structure can be deduced by comparing the experimental SAXS curve to
theoretical curves calculated from oligomer models identified by PISA or from
manual inspection. The FoXS server and CRYSOL are good tools for this. FoXS
also allows ensembles of oligomers (MES) to be used in fitting the data (e.g.
mixture of monomer + dimer). I believe ATSAS also has an ensemble program, but
the name escapes me at this time. We have used this approach to show that
assemblies that are predicted to be stable by PISA are not found in solution (3
and unpublished results).

1: Rambo RP, Tainer JA. Accurate assessment of mass, models and resolution by
small-angle scattering. Nature. 2013 Apr 25;496(7446):477-81. doi:
10.1038/nature12070. PubMed PMID: 23619693; PubMed Central PMCID: PMC3714217.

2: Rambo RP, Tainer JA. Characterizing flexible and intrinsically unstructured
biological macromolecules by SAS using the Porod-Debye law. Biopolymers. 2011
Aug;95(8):559-71. doi: 10.1002/bip.21638. Epub 2011 Apr 20. PubMed PMID:
21509745; PubMed Central PMCID: PMC3103662.

3: Luo M, Singh RK, Tanner JJ. Structural determinants of oligomerization of
δ(1)-pyrroline-5-carboxylate dehydrogenase: identification of a hexamerization
hot spot. J Mol Biol. 2013 Sep 9;425(17):3106-20. doi:
10.1016/j.jmb.2013.05.027.
Epub 2013 Jun 7. PubMed PMID: 23747974; PubMed Central PMCID: PMC3743950.

On Dec 12, 2014, at 4:56 AM, Jose Manuel Duarte wrote:

Dear Hay

Your post prompted me to respond, since I think the issue of symmetry is
extremely important.

I would like to reinstate here what should be obvious to everyone: a stable
asymmetric assembly of proteins in solution is essentially impossible (or at
most very very unlikely), purely because of topological reasons.

This is beautifully explained in a classic paper now 50 years old: Monod,
Wyman, Changeux (1965) On the Nature of Allosteric Transitions: A Plausible
Model. The reasoning there is that a homomeric protein in solution can only
associate in 2 ways: isologous (binding with same surface patches in both
monomers, necessarily through a 2-fold axis) or heterologous (binding through
different surface patches in both monomers). The isologous case is clearly
symmetric (C2). Whilst in the heterologous case the monomers can either
assemble infinitely or form a closed symmetry. The conclusion that follows is
that stable homo-oligomers can only be symmetric.

I especially like this paragraph:

On the basis of these considerations, it is reasonable to assume that, if an
oligomeric protein possesses a wide range of stability, it consists of a closed
structure where all the protomers use the same binding sets; which implies, as
we have just seen, that the molecule should possess at least one axis of
symmetry.

The paper really explains it a lot better than me, it can be found here:
http://www.pasteur.fr/ip/resource/filecenter/document/01s-4j-0er/monod-wyman-changeux-1965.pdf

The conclusion in any case is that asymmetry in homomers is, if not impossible,
highly unlikely. So in my opinion asymmetric assemblies should be proposed with
a lot of care, only if experimental data really is overwhelmingly clear. For
instance I don't think that gel filtration or AUC would be good evidence
enough: it really needs to be demonstrated that the interface that you see in
the crystal is the one leading to oligomerisation (perhaps with a mutagenesis
experiment?). Otherwise the interface in the crystal is most likely simply a
crystal contact.

Jose

On 12/12/14 10:15, Hay Dvir wrote:
Dear Jeremy,

Indeed, we also incline to think of it as a monomer in solution, but still
quite un-eased by the extensive interactions in the asu being merely as a
result of a crystallization artifact. As you said, we may need to rely more
heavily on biochemical analysis and since SEC wasn't clear we are turning now
to LS (hope to able to post a more conclusive update).

Regardless of what our final conclusion would be for this case, we became
rather generally interested to find other similar cases of homomeric assemblies
related only by non crystallographic translation symmetry (or as Engin Qzka
pointed out improper

Re: [ccp4bb] Phenix refinement

2014-11-26 Thread Tanner, John J.

Change ad to and in selection.

Sent from Jack's iPad

 On Nov 26, 2014, at 7:16 AM, Almudena Ponce Salvatierra 
 maps.fa...@gmail.com wrote:
 
 Dear all, 
 
 I am refining my structure with Phenix refine and I get the following error 
 message just before starting:
 
 no atom selected, name CA ad chain A and resname CA and resseq 1. 
 
 I knew how to fix it once but I think I have forgotten now. Anyway, the only 
 difference between the output model that came from the previous Phenix refine 
 run and this one (the input for the new run) is that I removed a Calcium ion 
 (this used to be chain A). So, if there is no chain A anymore, why does this 
 appear? I have no clue. 
 
 Any suggestions that will enable the continuation of this refinement will be 
 more than welcome. 
 
 Thanks a lot in advance. 
 
 Best wishes, 
 
 Almudena.
 
 -- 
 Almudena Ponce-Salvatierra
 Macromolecular crystallography and Nucleic acid chemistry
 Max Planck Institute for Biophysical Chemistry
 Am Fassberg 11 37077 Göttingen
 Germany

Re: [ccp4bb] Phenix refinement

2014-11-26 Thread Tanner, John J.

FYI, there is a phenix BB for phenix questions.

Sent from Jack's iPad

 On Nov 26, 2014, at 7:16 AM, Almudena Ponce Salvatierra 
 maps.fa...@gmail.com wrote:
 
 Dear all, 
 
 I am refining my structure with Phenix refine and I get the following error 
 message just before starting:
 
 no atom selected, name CA ad chain A and resname CA and resseq 1. 
 
 I knew how to fix it once but I think I have forgotten now. Anyway, the only 
 difference between the output model that came from the previous Phenix refine 
 run and this one (the input for the new run) is that I removed a Calcium ion 
 (this used to be chain A). So, if there is no chain A anymore, why does this 
 appear? I have no clue. 
 
 Any suggestions that will enable the continuation of this refinement will be 
 more than welcome. 
 
 Thanks a lot in advance. 
 
 Best wishes, 
 
 Almudena.
 
 -- 
 Almudena Ponce-Salvatierra
 Macromolecular crystallography and Nucleic acid chemistry
 Max Planck Institute for Biophysical Chemistry
 Am Fassberg 11 37077 Göttingen
 Germany

Re: [ccp4bb] modeling flexible ends on proteins

2014-10-24 Thread Tanner, John J.

Try I-TASSER and MODELER.

Sent from Jack's iPhone

 On Oct 24, 2014, at 9:17 AM, Michal Jamroz jam...@chem.uw.edu.pl wrote:
 
 Dnia 2014-10-22, o godz. 15:43:18
 Tommi Kajander tommi.kajan...@helsinki.fi napisał(a):
 
 Would anyone know a software to model (just with some kind of random
 coil) the amino acid chain for the assumed flexible disorderd regions
 between domains, or at one end of protein? just for illustrative
 purposes.
 
 Hi Tommi,
 
 check CABSflex: http://biocomp.chem.uw.edu.pl/CABSflex
 You can simply put there PDB code of considered structure and get info
 about flexibility, native-state dynamics movie, etc.
 
 Michał

Re: [ccp4bb] Merge PDB chains

2014-10-23 Thread Tanner, John J.

One option is to change the chain IDs and residue numbers manually using a text 
editor like nedit.

Sent from Jack's iPad

On Oct 23, 2014, at 6:03 AM, luzuok luzuo...@126.commailto:luzuo...@126.com 
wrote:

Dear all,
   Sorry to ask a simple question. There are many SO4 in my PDB file, one 
belongs to a different chain. I want to merge them into one chain, can anyone 
tell me how to do this?

Best regards!

Lu Zuokun




--
卢作�j
南开大学新生物站A202

Re: [ccp4bb] Protein model size is much bigger than EM map

2014-10-23 Thread Tanner, John J.

You could try situs colores, which  does fitting of model into map 
automatically.

Sent from Jack's iPhone

 On Oct 23, 2014, at 12:49 PM, jie liu jl1...@njms.rutgers.edu wrote:
 
 Dear you all
 
 May I ask a question? I tried to dock my protein structure onto an cryo-EM 
 density map. I loaded both the map file and my model coordinates into 
 Chimera. But it looks apparently that they are not in the same size scale. My 
 model is much bigger than the size of the EM map region where the model is 
 supposed to reside. I suspect the EM map size is scaled down somehow.
 
 I did a little research on internet but couldn't find a solution. Could you 
 please advice me how to put them to the same size scale?
 
 Your kind help is greatly appreciated!
 
 Jie

Re: [ccp4bb] PDB passes 100,000 structure milestone

2014-05-14 Thread Tanner, John J.

I agree with Mark.  The PDB should, at the very least, attach a warning label 
to entries like 2HR0, where the scientific community has overwhelmingly 
determined that the structure is invalid.  In this case, I believe the author 
never admitted any wrongdoing, and perhaps PDB policy prevents removal of the 
entry without the depositing author's consent.  I note that the PDB labels some 
structures associated with retracted papers as obsoleted and superseded by 
NONE.  For example, see 2qns and 2hlb.  

Jack


On May 14, 2014, at 12:06 PM, Tim Gruene wrote:

 Hi Mark,
 
 I understand the discussion, yet as far as I understand the PDB does not
 claim to be the authority to decide about the integrity of an entry (or
 maybe better said, the PDB claims not to be this authority), and I find
 it very honorable that the PDB have not abused their power. I don't mean
 such an authority should not exist, but I think it is a good think it is
 not the PDB. It is a form of separation of powers.
 
 Best,
 Tim
 
 On 05/14/2014 06:47 PM, Mark Wilson wrote:
 Hi Tim,
 I agree with everything you've said about the importance of validation,
 but aren't we really talking about something different here?  Users of
 structural information should of course be keeping a careful eye on
 validation reports. On the other hand, what possible reason is there for
 the PDB to continue to archive and offer for public use models whose
 fundamental integrity (rather than quality or reliability) are highly
 suspect?  I hope that I'm not the only one who is frustrated that the page
 for 2HR0 is still available and unblemished by warnings.
 Best regards,
 Mark
 
 Mark A. Wilson
 Associate Professor
 Department of Biochemistry/Redox Biology Center
 University of Nebraska
 N118 Beadle Center
 1901 Vine Street
 Lincoln, NE 68588
 (402) 472-3626
 mwilso...@unl.edu 
 
 
 
 
 
 
 On 5/14/14 11:35 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
 
 Dear Eric,
 
 On 05/14/2014 06:05 PM, Eric Williams wrote:
 [...]
 We seem to be at an impasse. The PDB won't evict highly suspect
 structure
 models unless journals retract them, and the journals in question have
 shown no indication of desiring to retract them. Is there anything that
 can
 be done? [...]
 
 What's the appropriate course of action for conscientious consumers of
 PDB
 data? Is there a way to petition journals to issue retractions? I wonder
 what the gents at Retraction Watch (http://retractionwatch.com) would
 recommend.
 
 Eric
 
 
 you can teach the consumers how to help themselves - you are welcome to
 join my session MS-84 at the IUCr 2014 :-) because I believe that one of
 the New Paradigms in Crystallography is the requirement to how to
 correctly interpret crystallographic models, and validation is becoming
 more and more important as subject.
 
 Best,
 Tim
 
 
 On Wed, May 14, 2014 at 10:04 AM, Bernhard Rupp
 
 hofkristall...@gmail.comhttps://mail.google.com/mail/?view=cmfs=1tf=1
 to=hofkristall...@gmail.com
 wrote:
 
 which structure ended up as number 100.000?
 I guess that depends if we still count the Murthy corpses like 2a01
 This
 3-armed Swastika for example still does not come with a single warning
 short of a poor quality report
 http://www.ebi.ac.uk/pdbe-srv/view/entry/2a01/summary_details.html So,
 sorry, 0 (or lessŠ.) valid entries only at the time of
 announcement.
 
 Cheers, BR
 
 
 
 Supplemental material:
 
 
 
 ³The PDB says it will remove the other ten structures only when
 editors at
 the journals in which they were originally published or the authors
 themselves retract them²
 
 *http://www.nature.com/news/2009/091222/full/462970a.html
 http://www.nature.com/news/2009/091222/full/462970a.html*
 
 
 
 
 
 ³With the support of the structural-biology community, the mission of
 the
 wwPDB is to safeguard the integrity and improve the quality of the PDB
 archive.²
 
 http://www.nature.com/nature/journal/v463/n7280/full/463425c.html
 
 
 
 Not to be overly cynical, but
 
 
 
 http://tinyurl.com/pmupalt
 
 
 
 
 
 *From:* CCP4 bulletin board
 [mailto:CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1
 tf=1to=CCP4BB@JISCMAIL.AC.UK]
 *On Behalf Of *mesters
 *Sent:* Mittwoch, 14. Mai 2014 14:42
 *To:* 
 CCP4BB@JISCMAIL.AC.UKhttps://mail.google.com/mail/?view=cmfs=1tf=1to
 =CCP4BB@JISCMAIL.AC.UK
 
 *Subject:* Re: [ccp4bb] PDB passes 100,000 structure milestone
 
 
 
 Amazing, great!
 
 And, which structure ended up as number 100.000?
 
 - J. -
 
 
 Am 14.05.14 10:42, schrieb battle:
 
 The Worldwide Protein Data Bank (wwPDB) organization is proud to
 announce
 that the Protein Data Bank archive now contains more than 100,000
 entries.
 
 Established in 1971, this central, public archive of
 experimentally-determined protein and nucleic acid structures has
 reached a
 critical milestone thanks to the efforts of structural biologists
 throughout the world.
 
 Read the full story at:
 http://www.wwpdb.org/news/news_2014.html#13-May-2014
 
 --
 Gary Battle
 on

[ccp4bb] Aggregation assay

2014-02-21 Thread Tanner, John J.

I am aware of an assay for aggregation (aggregation rate) that is based on 
fluorescence measurements.  It involves excitation at 280 and emission in the 
range 260-400. Is there a reference for the absorbance method?

See

Nominé Y, Ristriani T, Laurent C, Lefèvre JF, Weiss E, Travé G. A strategy for 
optimizing the monodispersity of fusion proteins: application to purification 
of recombinant HPV E6 oncoprotein. Protein Eng. 2001 Apr;14(4):297-305. PubMed 
PMID: 11391022.

http://www.ncbi.nlm.nih.gov/pubmed/11391022

Jack Tanner

Sent from Jack's iPad

On Feb 21, 2014, at 7:23 AM, Vivoli, Mirella 
m.viv...@exeter.ac.ukmailto:m.viv...@exeter.ac.uk wrote:

Dear Prerana,

before starting the crystallization you could try to check the state of you 
protein, simply determining the Aggregation Index (AI) from measuring the 
absorbance at 280 nm and 340 nm. The AI is then computed using this simple 
formula: AI= 100 x (Abs340/(Abs 280 - Abs 340)). Soluble and non-aggregated 
proteins solutions typically have an Aggregation Index of 2 and lower, whereas 
for some aggregation will be 2-5;  heavily aggregated proteins show an 
aggregation index 5. Of course you cannot use Nanodrop for it (because the 
wavelength for the baseline normalization is 340 nm). I would try to decrease 
the concentration of your protein to 4-5 mg/ml.Good luck.

Best,

Mirella


Vivoli Mirella

Postdoctoral Fellow
University of Exeter,
Biosciences
Biocatalysis Centre, Henry Wellcome Building
Stocker Road,
Exeter,
Ex4 4QD
Tel:+ 44 (0)1392 726121



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] 
on behalf of Prerana G. [tracy...@gmail.commailto:tracy...@gmail.com]
Sent: Friday, February 21, 2014 11:14 AM
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb]

Hi, Sorry for asking an off-topic question,
I have recently purified a protein having a molecular weight of 40kDa and 
concentration of the protein was 8mg/ml.  When I tried to set the protein for 
crystallisation using micobatch method, the protein started precipitating in 
most of the buffer conditions of Crystal screen and Peg ion. The precipitation 
took place very quickly (within 5-10 mins).
How should I overcome this problem?


Regards
Prerana

Re: [ccp4bb] suggestions for cryoprotectant

2014-02-06 Thread Tanner, John J.

Try L-proline.  It works well with high ionic strength conditions:

http://www.ncbi.nlm.nih.gov/pubmed/22868767

Sent from Jack's iPad

On Feb 6, 2014, at 10:40 PM, Deepak Thankappan Nair 
deepaktn...@gmail.commailto:deepaktn...@gmail.com wrote:

Hello,
Does anybody know what would be a good cryoprotectant for the following 
condition:
800 mM Sodium phosphate monobasic/1200 mM Potassium phosphate dibasic 100 mM 
Sodium acetate/Aceticacid pH4.5

Thanks
Deepak

Re: [ccp4bb] Best compounds for heavy atom soaks

2014-01-15 Thread Tanner, John J.

More references to consider…

You asked about soaking times - here are two articles advocating quick soaking 
at relatively high heavy atom concentration, which has worked well for us.  
We've had good luck with thimerosal.

Acta Crystallogr D Biol Crystallogr. 2002 Jul;58(Pt 7):1099-103. Epub 2002 Jun 
20.
Generating isomorphous heavy-atom derivatives by a quick-soak method. Part II: 
phasing of new structures.
Sun PD, Radaev S.

Acta Crystallogr D Biol Crystallogr. 2002 Jul;58(Pt 7):1092-8. Epub 2002 Jun 20.
Generating isomorphous heavy-atom derivatives by a quick-soak method. Part I: 
test cases.
Sun PD, Radaev S, Kattah M.

Petsko has a good discussion about the chemistry of heavy atom derivatization.

Methods Enzymol. 1985;114:147-56.
Preparation of isomorphous heavy-atom derivatives.
Petsko GA.
PMID: 4079763

Beck et al. would suggest you consider the triiodo magic triangle.

Acta Cryst. (2008). D64, 1179-1182[ doi:10.1107/S0907444908030266 ]
A magic triangle for experimental phasing of macromolecules
T. Beck, A. Krasauskas, T. Gruene and G. M. Sheldrick





John J. Tanner
Professor of Biochemistry and Chemistry
University of Missouri-Columbia
125 Chemistry Building
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-2754
Email: tanne...@missouri.edumailto:tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html

On Jan 15, 2014, at 11:32 AM, Engin Özkan 
eoz...@stanford.edumailto:eoz...@stanford.edu
 wrote:

There is quite a bit of literature on this, but my favorite paper is this:

http://www.ncbi.nlm.nih.gov/pubmed/18391402
Towards a rational approach for heavy-atom derivative screening in protein 
crystallography.

Spoiler: The overall winner is ethyl mercury phosphate (Figure 7). Of course, 
chemistry will dictate your success (as every article and book chapter on this 
topic stresses). Check out quick soak literature, but not halides like sodium 
bromide (less likely to work at your resolution).

Engin

On 1/15/14, 11:18 AM, RHYS GRINTER wrote:
Hello message board,

My group has some crystals of an interesting protein to take to the synchrotron 
in a couple of weeks. We won't be able to prepare and crystallise a SelMet 
derivative during that time period, but we have loads of crystals sitting 
around. The diffraction isn't great, we see maybe 3.5 at home but might be 
enough to get over the line.
It will be a very difficult MR target, so we were thinking of soaking so 
crystals with heavy atomic compounds that we have lying around. I was wondering 
if people had any suggestions of compounds that people have used successfully 
for experimental phasing and maybe concentrations to use and soaking time.

Cheers,

Rhys

Re: [ccp4bb] DNA Protein co- Crystallization

2014-01-04 Thread Tanner, John J.

We have limited experience in protein:DNA crystallization (N=1), but this is 
what worked for us a few years ago.

Like others have advised, I also suggest using oligos with different ends.  We 
tested two protein constructs,  one with a a TEVP cleavable N-terminal His tag 
and the other with a C-terminal His tag.   We used DNA purchased from IDT 
(standard desalting prep) without further purification.  Pairing two protein 
constructs with several different oligos meant that oligo cost was the limiting 
reagent.  We mixed the the protein and dsDNA in a ratio of protein:dsDNA=1:3, 
then ran size exclusion chromatography to isolate the complex.  Then we 
concentrated the complex and set up the standard crystal screens and Natrix.   
The details can be found in the Methods section and supplement of this paper:

http://www.ncbi.nlm.nih.gov/pubmed/18586269
J Mol Biol. 2008 Aug 1;381(1):174-88.
Structural basis of the transcriptional regulation of the proline utilization 
regulon by multifunctional PutA.
Zhou Y, Larson JD, Bottoms CA, Arturo EC, Henzl MT, Jenkins JL, Nix JC, Becker 
DF, Tanner JJ.

Good luck,

Jack


On Jan 3, 2014, at 10:23 PM, Acoot Brett wrote:

Dear All,

For the question, I think for a protein-DNA interaction, the protein may 
interact with any sequences of DNA, which will give a lot of combination of 
protein-DNA sequence for crystallization screening.  Or do anyone regard to 
just try the crystallization of the protein-one specific sequence DNA fragment 
for the trial (for example the DNA sequence with the highest binding affinity)? 
In another word, does the easiness of the crystallization has relation with how 
strong the protein interacts with the DNA sequence?

Acoot


On Saturday, 4 January 2014 11:02 AM, rajakumara eerappa 
reera...@gmail.commailto:reera...@gmail.com wrote:
My suggestions are
1 try complementary and non-complementary overhangs which can form Watson-crick 
and/ or Hoogstein base pairing.
2. If it binds self-complementary duplexes then try them also.
3. Peg conditions with slight acidic pH are more suitable.
4. Divalent cation salts (Ca, Mg, Mn) in crystallization.

Wish you good luck
Raj


On Friday, January 3, 2014, venkatareddy dadireddy wrote:
Hi,

I'm working on DNA binding protein, looking to co-crystallize protein- DNA 
complex and have no previous experience. Your suggestion would be very precious 
on the following queries.
1. My protein is 646 amino acid long and it exists as homodimer. It is also 
having around 20 amino acid extra sequence from vector. Will vector 
sequence affect   crystallization?
2. Its homologous protein shows good affinity for 31-mer. Shall I use same 
length   of DNA for co- crystallization.
3. What is the length of DNA to be used?
4. What is purity of oligos to be used? Is it HPLC pure or normal desalted 
ones. I have read on CCP4 mails for screening purpose normal oligos are 
fine. Please   comment on that.
3. Any other suggestions on Protein DNA co- crystallization.

Thanks
venkat

Re: [ccp4bb] Can Mathew's coefficient tell about a complex

2013-12-04 Thread Tanner, John J.

First of all, there are two Ts and no apostrophe in Matthews.  The method is 
based on the following paper, which is worth reading.  It is one of the first 
examples, possibly the first, of structural bioinformatics.

J Mol Biol. 1968 Apr 28;33(2):491-7.
Solvent content of protein crystals.
Matthews BW.
http://www.ncbi.nlm.nih.gov/pubmed/5700707

Secondly, you might run a gel on your crystals.


John J. Tanner
Professor of Biochemistry and Chemistry
University of Missouri-Columbia
125 Chemistry Building
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-2754
Email: tanne...@missouri.edumailto:tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html

On Dec 4, 2013, at 4:06 PM, abbas maqbool 
abbas_maqb...@yahoo.commailto:abbas_maqb...@yahoo.com
 wrote:

Dear All,
I crystallized a complex of two proteins and got x-ray data. However I dont 
know if I have got complex or just one of the protein has crystallized. Can I 
check it by mathew's coefficient? If yes how? One of my protein is 30 kDa nad 
other one is 12 kDa.
Actually I calculated Mathew's coeffient (based on Mol. wt of complex 42000 
Da), and results were like that


Cell Volume = 993567
Nmol/asymMathews coeff%solvent
13.94   68
21.9737
3 1.36


Can any one please explain what does it suggest?

Thanks
Abbas

[ccp4bb] molprobity

2013-11-11 Thread Tanner, John J.

I encountered the same problem last night.   The server won't upload the PDB 
file.  I didn't check this morning.


On Nov 11, 2013, at 10:02 AM, SD Y wrote:

Hi,

I was wondering if molprobity server is down 
(http://molprobity.biochem.duke.edu/index.php) or its just my files or our 
network has problem because I cant upload my files (some times it gave error).

Thanks
SDY



John J. Tanner
Professor of Biochemistry  and Chemistry
University of Missouri-Columbia
125 Chemistry Building
Columbia, MO  65211
email: tanne...@missouri.edumailto:tanne...@missouri.edu
phone: 573-884-1280
fax: 573-882-2754
web: http://www.chem.missouri.edu/tannergroup/tanner.html

Re: [ccp4bb] SA-omit map

2013-11-04 Thread Tanner, John J.

I have two bits of advice.

1. If the SA omit map for the ssDNA is really bad, perhaps you should 
reconsider whether your model is a faithful representation of the experimental 
data.

2. You could use anomalous difference Fourier analysis to locate the P atoms of 
the DNA backbone.   We did this for ssDNA bound to a Fab using a data set 
collected at wavelength=1.74 A.  See Figure 3 of

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2516951/


John J. Tanner
Professor of Biochemistry and Chemistry
University of Missouri-Columbia
125 Chemistry Building
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-2754
Email: tanne...@missouri.edumailto:tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html

On Nov 4, 2013, at 10:42 AM, Matthew Franklin 
mfrank...@nysbc.orgmailto:mfrank...@nysbc.org
 wrote:

Hi Deng -

Can you tell why the reviewer was asking for the SA-omit map?  Is there some 
doubt about the conformation of your ssDNA, or even whether it is present in 
the first place?  Is there a question about the sequence, or the sequence 
register (which nucleotides go in which positions)?

Even a poor-quality map should let you locate the phosphate backbone of the 
DNA.  This should convince most reviewers that the DNA is present and in the 
general position you have modeled.  You can't resolve concerns about nucleotide 
base position or conformation without a better quality map.

I imagine that you built the protein model first during your structure 
determination, and only added the ssDNA later in the refinement.  If this is 
correct, you could present the maps from the last refinement cycle before you 
added the DNA.  This is even less model biased than what the reviewer wants.

Hope that helps,
Matt



On 11/4/13 1:36 AM, dengzq1987 wrote:
Dear all,

 Recently, I received the comments from referees, they asked for the SA-omit 
map of the ssDNA of our protein-DNA complex. They said that simulated annealing 
omit map better than a biased 2Fo-Fc. The ssDNA consists of seven thymidine 
nucleotide. Our data diffracted to 2.65A，but the data quality is not good and 
twin. We tried to produce SA-omit map using phenix. The map is really bad. Does 
anyone have suggestion to refine the map?  Thank you!


Bests,
zq Deng
2013-11-04

dengzq1987



--
Matthew Franklin, Ph. D.
Senior Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(212) 939-0660 ext. 9374

Re: [ccp4bb] Problematic PDBs

2013-10-17 Thread Tanner, John J.

I use 2QNS for teaching. It is an egregious case of modeling ligand into noise.
Also, the structure has many close contacts (e.g. HOH A351), poor
stereochemistry (e.g. A58-A61), and incorrectly built water. Turn on symmetry
to see the steric clash of the peptide ligand with itself. You can get the
coordinates and maps from EDS.

http://www.ncbi.nlm.nih.gov/pubmed/18611381
http://www.ncbi.nlm.nih.gov/pubmed/21827955
http://retractionwatch.wordpress.com/2011/08/16/ties-that-dont-bind-group-retracts-parathyroid-hormone-crystallography-paper/
http://retractionwatch.wordpress.com/2012/01/26/pnas-retraction-marks-second-for-crystallography-group/

John J. Tanner
Professor of Biochemistry and Chemistry
University of Missouri-Columbia
125 Chemistry Building
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-2754
Email: tanne...@missouri.edumailto:tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html

On Oct 17, 2013, at 8:51 AM, Lucas
lucasbleic...@gmail.commailto:lucasbleic...@gmail.com
wrote:

Dear all,

I've been lecturing in a structural bioinformatics course where graduate
students (always consisting of people without crystallography background to
that point) are expected to understand the basics on how x-ray structures are
obtained, so that they know what they are using in their bioinformatics
projects. Practices include letting them manually build a segment from an
excellent map and also using Coot to check problems in not so good structures.

I wonder if there's a list of problematic structures somewhere that I could use
for that practice? Apart from a few ones I'm aware of because of (bad)
publicity, what I usually do is an advanced search on PDB for entries with poor
resolution and bound ligands, then checking then manually, hopefully finding
some examples of creative map interpretation. But it would be nice to have
specific examples for each thing that can go wrong in a PDB construction.

Best regards,
Lucas

Re: [ccp4bb] Docking models into low-res SAD map

2013-09-19 Thread Tanner, John J.

Perhaps Situs colores would be useful.  We use it to dock models into SAXS maps.

http://situs.biomachina.org/fguide.html


Sent from Jack's iPad

On Sep 18, 2013, at 5:48 PM, Oliver Clarke olibcla...@gmail.com wrote:

 Hi all,
 
 Can anyone recommend software to dock previously solved domains into a (very) 
 low-resolution experimentally phased map?
 
 I am working on a rather marginal case where this would be useful - very 
 large assembly (500kDA per ASU), native goes to 6.9A, and the best derivative 
 goes to 8A with SAD phases from a heavy atom cluster to 11. Unfortunately no 
 NCS is present.
 
 The map is (for the resolution!) not too bad - the solvent boundary is clear 
 after SHELXE, and I can manually place a previously solved structure and get 
 a reasonably convincing fit (and the fit I obtain agrees with that previously 
 determined using CryoEM by another group). 
 
 There are a couple of other domains that I would like to place, and I believe 
 I have some idea of where they are, but manual fitting is somewhat 
 subjective, so I'd like an automated routine for doing the same - something 
 like the functionality that ADP_EM provides when working with CryoEM maps. 
 Does something like this exist? I tried using ADP_EM but it gives a segfault 
 when used with a crystallographic density map.
 
 I have tried using MOLREP to look for the model in the map to no avail, and 
 PHASER didn't work either.
 
 On another note, if anyone has any tips for density modification/phase 
 extension in this resolution range I would love to hear them - haven't had a 
 whole lot of luck with PARROT, DM, or SOLOMON, the maps seem stuck at ~10A 
 despite data going to 8. I tried using SHARP with the SPHCLUSTER tag on, but 
 it gave no improvement over what I obtain treating the cluster as a super 
 atom in SHELXD.
 
 Many thanks in advance!
 
 Oliver.

Re: [ccp4bb] Crystallization condition for trimeric protein

2013-09-12 Thread Tanner, John J.

Perhaps you should try finding buffer conditions and protein concentration that 
pushes the self-association equilibrium to one particular oligomeric state.

Sent from Jack's iPad

On Sep 12, 2013, at 9:53 AM, Debasish Kumar Ghosh dkgh...@cdfd.org.in wrote:

 Hi,
 
 I am working with a protein which can assume different oligomerization forms, 
 starting from monomers to trimers and even penta-decamers. We conformed this 
 by Native PAGE and HPLC studies. The protein's theoretical monomeric 
 molecular weight is 14.6 KDa (pI - 5.9) and it has some 140 amino acids with 
 high Glutamic acid (24), Lysine (10) and Arginine (13) content. I have tried 
 to crystallize it but not getting any hit as far now.
 Previous study showed that this protein gets some stability by Calcium ion. 
 With the calcium chloride conditions, I am getting spherical shaped 
 structures, but not sure what are they; calcium chloride crystals or protein 
 crystals. Can protein crystals be spherical in shape, specially when the 
 protein behaves like an oligomer?
 Also please let me know what is the minimum protein concentration required to 
 obtain crystal for such small protein (if there is any empirical rule/idea).
 Any suggestion will be highly appreciated.
 
 Thanks and regards,
 Debasish Kumar Ghosh
 
 CSIR- Junior Research Fellow (PhD Scholar)
 C/o: Dr. Akash Ranjan
 Computational and Functional Genomics Group
 Centre for DNA Fingerprinting and Diagnostics
 Hyderabad, INDIA
 
 Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com
 Telephone: 0091-9088787619 (M), 0091-40-24749396 (Lab)
 Lab URL: 
 http://www.cdfd.org.in/labpages/computational_functional_genomics.html

Re: [ccp4bb] Substrate/Ligand Induced Oligomerization of enzymes

2013-08-08 Thread Tanner, John J.

Jaffe's morpheeins might be of interest to you.  Here is one paper:


http://www.ncbi.nlm.nih.gov/pubmed/15710608


Sent from Jack's iPad

On Aug 8, 2013, at 7:21 PM, Shiva Bhowmik gene1...@gmail.com wrote:

 Dear All,
 
 I am looking for references and/or example of substrate or ligand induced 
 oligomerization of enzymes related to activation. 
 
 Any help in this regard would be greatly appreciated.
 
 Thanks.
 
 Shiva

Re: [ccp4bb] cryo condition

2013-05-23 Thread Tanner, John J.

L-proline works well with ammonium sulfate:

http://www.ncbi.nlm.nih.gov/pubmed/22868767


Sent from Jack's iPad

On May 23, 2013, at 4:42 AM, Faisal Tarique faisaltari...@gmail.com wrote:

 
 Dear all
 
 Can anybody tell me the appropriate cryo condition for the crystals obtained 
 in 2M Ammonium sulphate and tris pH8.5..I tried to add 10% glycerol to it but 
 still the ice ring is forming..
 
 Thanx in advance
 -- 
 Regards
 
 Faisal
 School of Life Sciences
 JNU

Re: [ccp4bb] pKa and electrostatic affinity

2013-04-04 Thread Tanner, John J.

A good starting place:

Biophys J. 1996 Oct;71(4):2049-55.
Evaluation of linked protonation effects in protein binding reactions using 
isothermal titration calorimetry.
Baker BM, Murphy KP.

Abstract
A theoretical development in the evaluation of proton linkage in protein 
binding reactions by isothermal titration calorimetry (ITC) is presented. For a 
system in which binding is linked to protonation of an ionizable group on a 
protein, we show that by performing experiments as a function of pH in buffers 
with varying ionization enthalpy, one can determine the pK(a)'s of the group 
responsible for the proton linkage in the free and the liganded states, the 
protonation enthalpy for this group in these states, as well as the intrinsic 
energetics for ligand binding (delta H(o), delta S(o), and delta C(p)). 
Determination of intrinsic energetics in this fashion allows for comparison 
with energetics calculated empirically from structural information. It is shown 
that in addition to variation of the ligand binding constant with pH, the 
observed binding enthalpy and heat capacity change can undergo extreme 
deviations from their intrinsic values, depending upon pH and buffer conditions.
PMID: 8889179 [PubMed - indexed for MEDLINE] PMCID: PMC1233671

On Apr 4, 2013, at 8:56 AM, Deepak Oswal wrote:


Dear colleagues:

I was wondering if you could kindly share your thoughts and help me understand 
the relationship between pKa and affinity of a protein for a ligand. Are these 
two properties related? Specifically, does a lysine with a pKa of 8.5 have a 
greater affinity for a negatively charged ligand than a lysine with a pKa of 
10.5 for the same ligand at physiological pH?

Any comments would be highly appreciated.

Deepak

[ccp4bb] predicting membrane-association domain

2012-08-21 Thread Tanner, John J.

Sorry for the off-topic post…

Does anyone know of software that predicts the membrane-association domain of 
peripheral membrane proteins using sequence and/or atomic coordinates?

Thanks.


John J. Tanner
Professor of Chemistry and Biochemistry
University of Missouri-Columbia
125 Chemistry Building
Columbia, MO  65211
email: tanne...@missouri.edumailto:tanne...@missouri.edu
phone: 573-884-1280
fax: 573-882-2754
web: http://www.chem.missouri.edu/tannergroup/tanner.html

Re: [ccp4bb] NADP binding protein without Rossmann fold.

2012-08-12 Thread Tanner, John J.

Many flavin reductases and monooxygenases bind NAD(P)H without the Rossmann 
fold.  See the review by Massey (2000) The chemical and biological versatility 
of riboflavin. Biochem. Soc. Trans. 28(4):283-296. Also, ALDHs bind NAD(P)+ 
with a Rossmann-like fold, which is considered to be a nonclassical Rossmann 
fold.  See Liu, et al., Nat. Struct. Biol.  1997.   


On Aug 12, 2012, at 3:20 PM, Karsten Niefind wrote:

 Zitat von Sudipta Bhattacharyya sudiptabhattacharyya.iit...@gmail.com:
 
 Dear all,
 
 I have biochemically characterized one enzyme that can dephosphorylate
 NADP+ / NADPH. Recently, I have also solved the crystal structure of the
 protein with bound NADP+. The important thing is that, the protein do not
 have the Rossmann fold or the dinucleotide binding fold. Can any one please
 cite or suggest any other example of such type of anomaly? Is there any
 example of non-classical Rossmann fold bearing proteins?
 
 Thanks,
 Sudipta.
 
 
 Dear Sudipta,
 
 AKR enzymes (aldo/keto reductases; see www.med.upenn.edu/akr/ and 
 www.ncbi.nlm.nih.gov/pubmed/20887732) bind NAD(P) and have an (alpha/beta)8 
 barrel motif.
 
 Best wishes,
 
 Karsten Niefind
 
 
 -
 Karsten Niefind, PhD
 University of Cologne
 Department of Chemistry
 Otto-Fischer-Str. 12-14
 D-50674 Cologne
 Tel.: +49 (0)221 4706444
 Fax:  +49 (0)221 4703244

Re: [ccp4bb] Heterotetrameric protein

2012-02-25 Thread Tanner, John J.

Tryptophan synthase forms a ABBA tetramer (PDB 2J9X).  It is not exactly what 
you want, but it is different from what you have found. 

Jack Tanner

John J. Tanner
Professor of Chemistry and Biochemistry
University of Missouri-Columbia
125 Chemistry Building
Columbia, MO  65211
email: tanne...@missouri.edu
phone: 573-884-1280
fax: 573-882-2754
web: http://www.chem.missouri.edu/tannergroup/tanner.html

On Feb 25, 2012, at 6:26 PM, Koustav Maity wrote:

 
 
 
 
 Hi all,
 
   does anyone know a protein which make hetero tetramer of A2B2 which arrange 
 asno1.png  and NOT as no2.png?
   
 
 Its great if these proteins are small? All the hetero tetramer I found was of 
 no2.png type.
 
 
 Thanks
 
 Dhiraj

Re: [ccp4bb] Fwd: HR3699, Research Works Act

2012-02-16 Thread Tanner, John J.

There was an op-ed piece in the NY Times last month about this issue written by 
Michael Eisen, a found of PLos:

http://www.nytimes.com/2012/01/11/opinion/research-bought-then-paid-for.html?ref=carolynbmaloney



On Feb 16, 2012, at 9:47 AM, Paula Salgado wrote:

May I also suggest reading these:

https://intechweb.wordpress.com/2012/01/25/selected-reading-on-research-works-act-why-you-should-care/

https://intechweb.wordpress.com/2012/02/16/open-access-on-a-string-cut-it-and-it-will-grow-back/

Can non-US based scientists sign the petition, btw?


There are also several blogposts and discussions around regarding RWA
and subsequent calls for boycotts of publishers that support it. A few
examples (mostly from the UK):

http://cameronneylon.net/blog/the-research-works-act-and-the-breakdown-of-mutual-incomprehension/

http://gowers.wordpress.com/2012/01/21/elsevier-my-part-in-its-downfall/

http//www.elsevier.com/wps/find/intro.cws_home/elsevieropenletter

http//occamstypewriter.org/scurry/2012/02/12/an-open-letter-to-elsevier/

And my (very) personal views on the matter:
http://www.paulasalgado.org/archives/423

Best wishes
Paula

On 16 February 2012 15:24, Herbert J. Bernstein
y...@bernstein-plus-sons.com wrote:
The bill summary says:

Research Works Act - Prohibits a federal agency from adopting, maintaining,
continuing, or otherwise engaging in any policy, program, or other activity
that: (1) causes, permits, or authorizes network dissemination of any
private-sector research work without the prior consent of the publisher; or
*(2) requires that any actual or prospective author, or the author's
employer, assent to such network dissemination. *

Defines private-sector research work as an article intended to be
published in a scholarly or scientific publication, or any version of such
an article, that is not a work of the U.S. government, describing or
interpreting research funded in whole or in part by a federal agency and to
which a commercial or nonprofit publisher has made or has entered into an
arrangement to make a value-added contribution, including peer review or
editing, but does not include progress reports or raw data outputs routinely
required to be created for and submitted directly to a funding agency in the
course of research.

==

It is the second provision that really cuts the legs out from the NIH open
access policy. What the NIH policy does is to make open access publication a
condition imposed on the grant holders in publishing work that the NIH
funded. This has provided the necessary lever for NIH-funded authors to be
able to publish in well-respected journals and still to be able to require
that, after a year, their work be available without charge to the scientific
community. Without that lever we go back to the unlamented old system (at
least unlamented by almost everybody other than Elsevier) in which pubishers
could impose an absolute copyright transfer that barred the authors from
ever posting copies of their work on the web. People affiliated with
libraries with the appropriate subscriptions to the appropriate archiving
services may not have noticed the difference, but for the significant
portions of both researchers and students who did not have such access, the
NIH open access policy was by itself a major game changer, making much more
literature rapidly accessible, and even more importantly changed the
culture, making open access much more respectable.

The NIH policy does nothing more than put grant-sponsored research on almost
the same footing as research done directly by the government which has never
been subject to copyright at all, on the theory that, if the tax-payers
already paid for the research, they should have open access to the fruits of
that research. This law would kill that policy. This would be a major step
backwards.

Please read:

http://blogs.scientificamerican.com/evo-eco-lab/2012/01/16/mistruths-insults-from-the-copyright-lobby-over-hr-3699/

http://www.taxpayeraccess.org/action/action_access/12-0106.shtml

http://www.care2.com/causes/open-access-under-threat-hr-3699.html

Please support the petition. This is a very bad bill. It is not about
protecting copyright, it is an effort to restrict the free flow of
scientific information in our community.

Regards,
Herbert

On 2/16/12 9:02 AM, Fischmann, Thierry wrote:

Herbert

I don't see how the act could affect the NIH open access policy. Could you
please shed some light on that?

What I read seems reasonable and I intend to ask my representatives to
support this text. But obviously I am missing something and like to learn
from you first.

Regards
Thierry


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Herbert J. Bernstein
Sent: Thursday, February 16, 2012 8:16 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fwd: HR3699, Research Works Act

Dear Ian,

   You are mistaken.  The proposed law has nothing to do with

Re: [ccp4bb] how can merge two PDB

2011-10-19 Thread Tanner, John J.

3 ways:

cat mol1 mol2  mol3

Use an editor such as nedit to cut and paste.

Coot merge molecules function.

Sent from Jack's iPad

On Oct 19, 2011, at 8:13 AM, Afshan Begum 
afshan...@yahoo.commailto:afshan...@yahoo.com wrote:

Hello CCP4 user

I have collected a data set 2.1 for my complex. Actually after  first run of 
Rafmac i can see the density for my inhibitor but the problem is my inhibitor 
is 6 KDa and i know the sequence of my inhibitor as well this inhibitor already 
crystallize with other protein molecule present in PDB data bank so how can i 
put in to that electron density i mean are there any ways to combine two Pdb in 
one molecule?

I would be thankful for your help



Best Regards

AFSHAN

Re: [ccp4bb] Low resolution structure determination advice

2011-09-02 Thread Tanner, John J.

Did you try density modification starting with the sad phases with phase 
extension to 2.7 A followed by auto-tracing?  The model should be better than 
the one built from the 3.7 A sad map.



Sent from Jack's iPad

On Sep 1, 2011, at 11:24 PM, Kianoush Sadre-Bazzaz 
ksad...@yahoo.commailto:ksad...@yahoo.com wrote:

Hi Basu,

You mentioned molecular replacement was not successful for this project. Which 
model was used for this procedure? Have you tried your partially built 
structure as a model to obtain preliminary phases for your native (2.7A) data 
set? If there is  any luck with that, you might be able to combine phases from 
this procedure with the Selenium SAD phases, as already suggested.

Kianoush

--- On Thu, 9/1/11, Basudeb Bhattacharyya 
bbhattach...@wisc.edumailto:bbhattach...@wisc.edu wrote:

From: Basudeb Bhattacharyya 
bbhattach...@wisc.edumailto:bbhattach...@wisc.edu
Subject: [ccp4bb] Low resolution structure determination advice
To: mailto:CCP4BB@JISCMAIL.AC.UK 
CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Date: Thursday, September 1, 2011, 9:31 AM

Dear all,

We're looking for some advice about how to proceed with a structure we're 
working on.  Our protein is 750 amino acids and naturally binds zinc.  We have 
a SeMet data set that goes down to 3.7 angstroms.  4 of 8 selenium sites are 
ordered and visible in addition to our zincs and we've modeled about 450 
residues of C-alpha backbone off a pure SAD density map
(we've tried other phasing experiments such as Zn SAD, MAD, etc. and the best 
maps--clear density and visible secondary structures--we get are off Se SAD).  
We have one monomer per AU (and we have secondary structure coverage over our 
entire protein based on looking at conserved domains of our 
protein--unfortunately, MR is not working for this project).
R/Rfree hits a minimum of 37/41 respectively in spacegroup P32 (we've tried P3 
and P31, which haven't worked).  We also have a native set down to 2.7 
angstroms.  We are able to place our working model into the native data set, 
but we are unable to further refine the structure in Refmac (density doesn’t 
improve and the stats creep up).  Addition of side chains only makes our stats 
worse.  The data sets are clean (no twinning, etc.).  While we understand that 
we may need more phasing information (i.e. our initial model may still be quite 
inaccurate given resolution and size of the protein among other things--we are 
trying to improve this), we're wondering if anyone might have some other 
suggestions or insights about how we can move forward given the data that we 
currently have. Thanks in advance for any advice.

Sincerely,

Basu

[ccp4bb] Coot density fit analysis with mtz from PHENIX 1.6.4

2010-11-27 Thread Tanner, John J.

Dear CCP4BB,

Has anyone encountered the following problem when using Coot (coot-0.6.2pre) 
validate density fit analysis with an mtz file calculated using phenix.refine 
(1.6.4)?

All of the density fit values are exactly 0.0 (all bars same height and red) 
when using a 2Fo-Fc map calculated from an mtz file output by PHENIX Version: 
1.6.4, Release tag: 486, Platform: intel-linux-2.6 redhat-e5.5.  Density fit 
analysis worked fine when I was using mtz files from PHENIX Version: 1.6.2, 
Release tag: 432, Platform: intel-linux-2.6 redhat-e5.5.  Thus, it appears to 
be an issue with the new version of phenix.  I should mention that the maps 
from 1.6.4 mtz files display fine in Coot and real space refinement against 
those maps in Coot works fine too.  It is just the density fit analysis utility 
that seems to be problematic.

Thanks,

Jack Tanner


--
John J. Tanner
Professor of Chemistry and Biochemistry
University of Missouri-Columbia
125 Chemistry Building
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-2754
Email: tanne...@missouri.edu
http://www.chem.missouri.edu/TannerGroup/tanner.html

Re: [ccp4bb] relationship between B factors and Koff

2010-11-19 Thread Tanner, John J.

This doesn't directly address your question, but since the subject of analyzing 
protein-protein interactions with gel filtration is raised on this bb 
occasionally, I thought I would mention that there are cases in which 
conventional gel filtration chromatography fails to provide evidence of a known 
protein:protein interaction.  In such cases, the Hummel-Dreyer gel filtration 
method is sometimes used.  It involves supplementing the running buffer with 
one of the proteins, so you need a lot of protein.  Here are two references:

Proc. Natl. Acad. Sci. USA 88 (1991)
Biochemisrry (1993) 32, 11124-11131


On 11/19/10 6:58 AM, Sebastiano Pasqualato 
sebastiano.pasqual...@ifom-ieo-campus.it wrote:

Hi all,
I have a crystallographical/biochemical problem, and maybe some of you guys can 
help me out.

We have recently crystallized a protein:protein complex, whose Kd has been 
measured being ca. 10 uM (both by fluorescence polarization and surface plasmon 
resonance).
Despite the 'decent' affinity, we couldn't purify an homogeneous complex in 
size exclusion chromatography, even mixing the protein at concentrations up to 
80-100 uM each.
We explained this behavior by assuming that extremely high Kon/Koff values 
combine to give this 10 uM affinity, and the high Koff value would account for 
the dissociation going on during size exclusion chromatography. We have partial 
evidence for this from the SPR curves, although we haven't actually measured 
the Kon/Koff values.

We eventually managed to solve the crystal structure of the complex by mixing 
the two proteins (we had to add an excess of one of them to get good 
diffraction data).
Once solved the structure (which makes perfect biological sense and has been 
validated), we get mean B factors for one of the component (the larger) much 
lower than those of the other component (the smaller one, which we had in 
excess). We're talking about 48 Å^2 vs. 75 Å^2.

I was wondering if anybody has had some similar cases, or has any hint on the 
possible relationship it might (or might not) exist between high a Koff value 
and high B factors (a relationship we are tempted to draw).

Thanks in advance,
best regards,
ciao
s


--
Sebastiano Pasqualato, PhD
IFOM-IEO Campus
Dipartimento di Oncologia Sperimentale
Istituto Europeo di Oncologia
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5094
fax +39 02 9437 5990

[ccp4bb] Fill map/mask with dummy atoms?

2010-10-13 Thread Tanner, John J.

Flood fills a map with water molecules.

http://xray.bmc.uu.se/usf/flood_man.html


On 10/13/10 6:49 AM, Dirk Kostrewa kostr...@genzentrum.lmu.de wrote:



  ... maybe, to clarifiy my question a little bit: I want to fill an
essentially flat cryo-EM-map with dummy atoms. So, a peak search doesn't
work. I would need a program that fills this map with dummy atoms for a
few things that I want to try with this atomic representation.

Best regards,

Dirk.

Am 13.10.10 13:00, schrieb Dirk Kostrewa:
  Dear CCP4ers,

 is there a program around that allows to fill an input map or mask
 with dummy atoms?

 Best regards,

 Dirk.


--

***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***

[ccp4bb] Off-topic: hollow protein crystals

2010-06-02 Thread Tanner, John J.

Kurt Krause's group solved a structure from hollow crystals:

J. Mol. Biol. 2002 Apr 26;318(2):503-18.
The crystal structure of Trichomonas vaginalis ferredoxin provides insight into 
metronidazole activation.
Crossnoe CR, Germanas JP, LeMagueres P, Mustata G, Krause KL.




From: Andre Ambrosio andre.ambro...@cebime.org.br
Reply-To: Andre Ambrosio andre.ambro...@cebime.org.br
Date: Wed, 2 Jun 2010 14:07:14 -0500
To: CCP4BB@JISCMAIL.AC.UK
Conversation: [ccp4bb] Off-topic: hollow protein crystals
Subject: [ccp4bb] Off-topic: hollow protein crystals

Dear all,

We have recently obtained crystals from a small protein, and interestingly, at 
least for me, they are hollow trigonal rods (please see pictures attached).
Just out of curiosity, has anybody ever seen such feature for protein crystals 
before?

Regards,
-Andre.

Re: [ccp4bb] Possible sulphate

2010-04-07 Thread Tanner, John J.

A reasonably strong peak on the S atom in an anomalous difference Fourier map.

From: Rex Palmer rex.pal...@btinternet.com
Reply-To: Rex Palmer rex.pal...@btinternet.com
Date: Wed, 7 Apr 2010 09:00:59 -0500
To: CCP4BB@JISCMAIL.AC.UK
Conversation: [ccp4bb] Possible sulphate
Subject: [ccp4bb] Possible sulphate

What seems to be a possible sulphate has been identified in our electron 
density.
What steps could/should be taken to confirm or consolidate this assignment that 
would satisfy referees?

Rex Palmer
Birkbeck College

[ccp4bb] Retraction of 12 Structures

2009-12-10 Thread Tanner, John J.

Some of you might be curious about the Ajees et al debacle that Jacob 
mentioned in his message.  Here are two links:

Nature Brief Communication that questioned the validity of one of  Murthy's 
structures:

http://www.nature.com/nature/journal/v448/n7154/full/nature06102.html

Murthy's rebuttal:

http://www.nature.com/nature/journal/v448/n7154/full/nature06103.html

Jack


--
John J. Tanner
Professor of Chemistry and Biochemistry
University of Missouri-Columbia
125 Chemistry Building
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-2754
Email: tanne...@missouri.edu
http://www.chem.missouri.edu/TannerGroup/tanner.html


From: Jacob Keller j-kell...@md.northwestern.edu
Reply-To: Jacob Keller j-kell...@md.northwestern.edu
Date: Thu, 10 Dec 2009 11:59:49 -0600
To: CCP4BB@JISCMAIL.AC.UK
Conversation: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures

I assume this is the denouement of the Ajees et al debacle a while back?
Does this mean all authors on all of those papers were complicit? Otherwise,
how would one author alone perpetrate this kind of thing? He pretends to go
to the synchrotron, comes back with the hkl file, and goes from there? What
about the crystals? Grows some lysozyme crystals, labels as protein x,
proceeds to go to the synchrotron and then...? This whole thing is really
hard to imagine--is there an initiation procedure in that lab, when the
noble lie is revealed to all would-be authors?

Jacob Keller

***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***

- Original Message -
From: Ibrahim Moustafa i.moust...@psu.edu
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thursday, December 10, 2009 8:16 AM
Subject: [ccp4bb] FW: pdb-l: Retraction of 12 Structures


 Hi all,

   I want to share the following e-mail received from pdb-l.

  It is sad to see something like that!

  regards,
 Ibrahim


 -- Forwarded Message
 From: Michael Sadowski mockeldri...@yahoo.com
 Date: Thu, 10 Dec 2009 04:22:28 -0800 (PST)
 To: pd...@rcsb.org
 Subject: pdb-l: Retraction of 12 Structures

 Dear All,

 Better check your data!

 Apologies to those who have seen this.

 S.

 -

 The University of Alabama at Birmingham has issued a statement indicating
 that a former UAB researcher may have fabricated or falsified data about
 protein structures that are contained in the Protein Data Bank.

 The university did not include a name of the researcher, but the
 Birmingham
 News this week reported that the scientist is H.M. Krishna Murthy and an
 independent review by BioInform of the PDB shows that Murthy is associated
 with all of the proteins that UAB said were falsified.

 The newspaper said that a probe of Murthy's research has been underway
 since
 2007.

 After a thorough examination of the available data, which included a
 re-analysis of each structure alleged to have been fabricated, the
 committee
 found a preponderance of evidence that structures 1BEF, 1CMW, 1DF9/2QID,
 1G40, 1G44, 1L6L, 2OU1, 1RID, 1Y8E, 2A01, and 2HR0 were more likely than
 not
 falsified and/or fabricated and recommended that they be removed from the
 public record, the university said in its statement this week.

 -
 http://www.genomeweb.com/informatics/university-alabama-says-researcher-fabr
 icated-protein-structures-now-protein-dat?utm_source=feedburnerutm_medium=f
 eedutm_campaign=Feed%3A+genomeweb%2Fbioinform+%28BioInform%29


 http://main.uab.edu/Sites/reporter/articles/71570/

 http://blog.al.com/birmingham-news-stories/2009/12/ex-uab_researchers_work_m
 ay_be.html




 TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see
 https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l .


 -- End of Forwarded Message

[ccp4bb] Mounting needle-shaped crystals

2009-10-05 Thread Tanner, John J.

Dear CCP4,

I'm looking for advice on mounting thin needles for low temperature data
collection. Our needles are fairly long (100-200 microns) but only 20
microns or less thick.  When I pick them up with Hampton loops (0.05-0.1 mm
size), the crystals tend to break as they are moved out of the drop and
through the liquid-air interface.

I see that Mitegen sells MicroLoops E, which are advertised as working well
for mounting needles.  Can anyone recommend them?  Can anyone recommend
Mitegen MicroMeshes or another tool for mounting needles?

Thanks,

Jack Tanner


-- 
John J. Tanner
Professor of Chemistry and Biochemistry
University of Missouri-Columbia
125 Chemistry Building
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-2754
Email: tanne...@missouri.edu
http://www.chem.missouri.edu/TannerGroup/tanner.html

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