Re: [ccp4bb] making a paper model

[Clement Angkawidjaja]

Dear Alice,

Instead of printing on paper, why not 3D-print it?

Cheers,
Clement

-Original Message- 
From: Alice Clark

Sent: Friday, March 10, 2017 1:18 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] making a paper model

Dear All,
How can I get a 2D net diagram from a 3D PDB structure, to make a paper 
model?


What I want to do is: take a 3D structure (GFP for Eg, PDB:4xow) make
a 2D image, print it on paper, roll it up to give the 3D structure of
the beta barrel - made of paper.

I have tried conventional topology programs but they "straighten" the
strands, so when you roll it up, the strands do not curve round the
barrel as they should. I can force this manually (cut and paste etc) -
but was hoping someone knows a way of doing it, in one step, within a
program. Perhaps using a 2D net image generator or similar?

All the best,
Alice 

Re: [ccp4bb] ANODE anomalous map in pymol

[Clement Angkawidjaja]

Have you tried changing the file extension to .ccp4 instead of .map?

Cheers,
Clement

From: Appu kumar 
Sent: Wednesday, March 01, 2017 7:54 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] ANODE anomalous map in pymol

Hi,

I Already did that in COOT, but PYMOL does not read it in map format. Pymol 
fail to show mesh in isomesh command. 

Thank you


Appu


On 28 February 2017 at 16:31, Paul Emsley  wrote:

  On 28/02/2017 20:44, Appu kumar wrote:

Dear CCP4 Users,
I ran anode to calculate the anomalous map for heavy atoms in protein. 
ANODE output the
anomalous map in .pha file, which can be viewed in COOT. However, I want to 
get the
anomalous map from .pha file to .map or .xplor file, which can be feed into 
PYMOL to make
maps. Is there a way to extract the anomalous map information from .pha 
file to .map or
.xplor file.


  In Coot:

  File -> Export Map

Re: [ccp4bb] Nitrate versus Carbonate

[Clement Angkawidjaja]

Maybe the Ca is just there as an additional binding site for carbonate.
Btw, are you looking at CmpA/NrtA? 

Cheers,
Clement

From: Keller, Jacob 
Sent: Friday, November 11, 2016 2:51 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Nitrate versus Carbonate

Well, I was looking at two periplasmic binding proteins, one for NO3 and one 
for CO3/HCO3, and was wondering whether the obligate cooperative Ca ion 
adjacent to the ligand only in the CO3 binder was necessary, and how in any 
case it would help distinguish the two if at all. Roger’s comments about CA are 
interesting in light of this, since there is no Ca ion involved (from what he 
said), and still CA binds so specifically to HCO3 and not NO3. I wonder whether 
the Ca ion protein I am looking at is specific for CO3 alone? I have seen this 
Ca ion phenomenon also in a lactate binding protein. Or maybe the Ca ion just 
makes the affinity much stronger than in CA’s?

 

Jacob Pearson Keller

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Clement 
Angkawidjaja
Sent: Friday, November 11, 2016 12:11 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Nitrate versus Carbonate

 

Dear JPK

 

What I know is we do not have much nitrate in the blood unlike 
carbonate/bicarbonate. 

Nitrite, a nitrate byproduct can cause problems but it has a different 
structure and probably does not interfere with bicarbonate binding to relevant 
proteins.

 

Cheers,

Clement

 

From: Keller, Jacob 

Sent: Friday, November 11, 2016 5:41 AM

To: CCP4BB@JISCMAIL.AC.UK 

Subject: [ccp4bb] Nitrate versus Carbonate

 

Dear Crystallographers,

 

I don’t think there is any feasible way crystallographically to distinguish 
between nitrate and carbonate or bicarbonate—correct? But that is not my main 
question.

 

My main question is: given that nitrate and carbonate are both very important 
and also very different physiologically, and therefore they must be 
distinguished/recognized by cells, how is this done, since the ions are so 
similar in structure? Is there some aspect of these ions that differs 
dramatically of which I am not aware? What kind of “handles” could a protein 
grab onto to distinguish between nitrate and carbonate/bicarbonate?

 

JPK

 

 

***

Jacob Pearson Keller, PhD

Research Scientist

HHMI Janelia Research Campus / Looger lab

Phone: (571)209-4000 x3159

Email: kell...@janelia.hhmi.org

***

 

Re: [ccp4bb] Nitrate versus Carbonate

[Clement Angkawidjaja]

Dear JPK

What I know is we do not have much nitrate in the blood unlike 
carbonate/bicarbonate. 
Nitrite, a nitrate byproduct can cause problems but it has a different 
structure and probably does not interfere with bicarbonate binding to relevant 
proteins.
Cheers,
Clement

From: Keller, Jacob 
Sent: Friday, November 11, 2016 5:41 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Nitrate versus Carbonate

Dear Crystallographers,

 

I don’t think there is any feasible way crystallographically to distinguish 
between nitrate and carbonate or bicarbonate—correct? But that is not my main 
question.

 

My main question is: given that nitrate and carbonate are both very important 
and also very different physiologically, and therefore they must be 
distinguished/recognized by cells, how is this done, since the ions are so 
similar in structure? Is there some aspect of these ions that differs 
dramatically of which I am not aware? What kind of “handles” could a protein 
grab onto to distinguish between nitrate and carbonate/bicarbonate?

 

JPK

 

 

***

Jacob Pearson Keller, PhD

Research Scientist

HHMI Janelia Research Campus / Looger lab

Phone: (571)209-4000 x3159

Email: kell...@janelia.hhmi.org

***

 

Re: [ccp4bb] Superpose program in CCP4

[Clement Angkawidjaja]

Dear Wenhe,

Have you looked at the Additional Log File from Superpose?

Cheers,
Clement

-Original Message- 
From: WENHE ZHONG

Sent: Sunday, October 30, 2016 12:47 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Superpose program in CCP4

Dear all,

I always use the SUPERPOSE tool in CCP4 to superpose molecules. This time I 
want to use the RMSD values of superposed C-alpha atoms to plot a RMSD graph 
(instead of using the graph automatically made by the program). However, 
there are many atoms missing in the RMSD list.


In the settings I chose “Superpose specific atoms/residues”, checked 
“Output all distances to a file”, fit “C-alpha atoms”. The superposed 
structures have exactly the same sequence.


My question is: is there any way to get the completed list of RMSD value for 
each C-alpha atom? Or is there any other program for this purpose?


Thank you!

Kind regards,
Wenhe 

Re: [ccp4bb] Electron density server

[Clement Angkawidjaja]

Dear Rojan,

Get the mmCIF, then use CIF2MTZ from CCP4.

Cheers,
Clement

On 10/25/13 3:07 PM, Rojan Shrestha wrote:


Hello,

Is EDS (electron density server) dead? In the absence of EDS, how can 
be mtz file directly downloaded?


Regards,

Rojan

Re: [ccp4bb] The binding between disordered and ordered proteins

[Clement Angkawidjaja]

Dear Dee,

Some proteins with chaperone-like activity (perhaps your B?) can only 
bind to partially folded proteins.
Probably A folds to a molten globule structure after 1-2 days. You can 
check by spectroscopic techniques (ANS or Trp fluorescence, CD).

Hope that helps.

Cheers,
Clement

On 10/22/13 11:10 AM, Xiaodi Yu wrote:

Dear All:

I have a general question about protein- protein interactions. I have 
two proteins, A and B. A is a disordered protein while B is a well 
folded protein. The binding between A and B has been approved by 
GST-pull down assay previously. The strange thing is I cannot get them 
bind if protein A were just freshly prepared. However, if I kept these 
two proteins separately for one or two days at 4 degree and then did 
the GST-pull down assay again, I can observe very strong interaction 
between A and B.


Protein A doesn't contain any cys residue. I have already test certain 
chemicals which might affect the interactions, for example, DTT and 
EDTA. These chemicals seems to have no effect on the binding.


Although A is a disordered protein, does it need such long time to 
find its proper conformation?


Do any people have similar experience? Any suggestions are greatly 
appreciated.


Thanks,

Dee

Re: [ccp4bb] On pKa of Aspartic acid

[Clement Angkawidjaja]

Hi Deepak,

Assuming that you have done the necessary things to measure the pKr of 
that particular Asp, I would say that the increase is advantageous for 
your enzyme. Enzyme catalysis often involves very subtle changes on the 
ionization state of the active site. But you need to be very careful in 
proposing a catalysis mechanism.


b) How is pKa related to an amino acids’ ability to force a water 
molecule to donate a proton?
Are you sure that the water donates a proton? Was your resolution high 
enough to observe it? How did you measure that pKr, by the way?


c) At pH 7.4, the aspartic acid would be de-protonated irrespective of 
whether the pKa is 3.8 or 6.44; isn’t that true?
I would say that the dominant fraction of Asp is deprotonated. But as 
you can see in the papers below, the pKr of Asp can vary from 0.5 to 9.2 
in folded proteins.


d) Have similar increase in pKa values observed for aspartic acids before?
there are some papers by Nick Pace's group:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2708032/?tool=pubmed
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2679426/?tool=pubmed
http://www.sciencedirect.com/science/article/pii/S002228360600934X

Cheers,
Clement

--


On 2/7/12 8:48 PM, Deepak Oswal wrote:


Dear colleagues,

We have solved the crystal structure of a human enzyme. The pKa of a 
catalytically critical aspartic acid has increased to 6.44. It is 
hydrogen bonded (2.8 Angstroms) to a water molecule that is supposed 
to donate a proton during the catalysis. Can anybody help me a) 
interpret the significance of this increase in pKa of the aspartic 
acid from 3.8 to 6.44 in context with the catalysis? Is this 
advantageous or detrimental? b) How is pKa related to an amino acids’ 
ability to force a water molecule to donate a proton? c) At pH 7.4, 
the aspartic acid would be de-protonated irrespective of whether the 
pKa is 3.8 or 6.44; isn’t that true? d) Have similar increase in pKa 
values observed for aspartic acids before? I would be grateful if 
anybody could explain or comment on the above queries.


Deepak Oswal

Re: [ccp4bb] Two different asymmetric units from two different crystallization conditions

[Clement Angkawidjaja]

Dear Shiva,

It has happened many times. This paper (not about crystallography) is one 
example: 
http://onlinelibrary.wiley.com/doi/10./j.1742-4658.2005.05047.x/abstract;jsessionid=864D79CC1089210C6A3CDDAC3AFE25DB.d03t04

Why don't you try SEC with high salt concentration?

Yours,
Clement

On Jun 9, 2011, at 3:19 AM, Shiva Bhowmik wrote:

 Dear All,
 
 I am working on a protein structure that yielded comparable diffraction 
 quality crystals from two different crystallization condition. One of the 
 crystallization condition conatins high conc. of  salt pptant whereas the 
 oher one contains high conc. of organic pptant. There are some minor 
 differences in the stucture with respect to the backbone but what most 
 surprising is the oligomeric structure. AnSEC study suggest the protein to be 
 a tetramer in solution and a tetrameric assembly is observed in the 
 asymmetric unit of the space group of the crystal obtained from high conc. of 
 organic pptant. However, the crystal structure from the high conc. of salt 
 pptant does not reveal any oligomeric assembly - symmetry operations of the 
 space group does not suggest any oligomeric assembly. I believe the high salt 
 conc. disrupted the tetrameric assembly and enabled crystallization of the 
 protein as a monomer. 
 
 Curious to know if there has been any similar precedence before.
 
 Cheers,
 
 Shiva


Clement Angkawidjaja, PhD.
G30 Assistant Professor
---
Chemistry-Biology Combined Major Program
International College, Osaka University
1-30 Machikaneyama-cho
Toyonaka, Osaka 560-0043, Japan
http://cmp.sci.osaka-u.ac.jp/CMP/
Tel. +81-6-6850-5952
Fax +81-6-6850-5961
---
Laboratory of Molecular Biotechnology
Graduate School of Engineering Osaka University
2-1 Yamadaoka U1E-804
Suita, Osaka 565-0871, japan
http://www.mls.eng.osaka-u.ac.jp/~bio_ext/mlsbe123/clement.html
Tel/Fax +81-6-6879-4157

Re: [ccp4bb] how to remove part of data with bad signal to noise ratio

[Clement Angkawidjaja]

Hi Seema,

Small addition to the already abundant suggestions, if you have high solvent 
content or significant portion of non-observable density, you normally get 
higher R-free.

Clement


Clement Angkawidjaja, PhD.
G30 Assistant Professor
---
Chemistry-Biology Combined Major Program
International College, Osaka University
1-30 Machikaneyama-cho
Toyonaka, Osaka 560-0043, Japan
http://cmp.sci.osaka-u.ac.jp/CMP/
Tel. +81-6-6850-5952
Fax +81-6-6850-5961
---
Laboratory of Molecular Biotechnology
Graduate School of Engineering Osaka University
2-1 Yamadaoka U1E-804
Suita, Osaka 565-0871, japan
http://www.mls.eng.osaka-u.ac.jp/~bio_ext/mlsbe123/clement.html
Tel/Fax +81-6-6879-4157

Re: [ccp4bb] how to remove part of data with bad signal to noise ratio

[Clement Angkawidjaja]

But you have to do solvent flattening (density modification), which people 
often (unintentionally?) skip for structures solved with molecular replacement. 
Please correct me if I am wrong.

Clement

On May 24, 2011, at 6:01 PM, herman.schreu...@sanofi-aventis.com wrote:

 This is not my experience. Provided the solvent is featureless, I find
 that a high solvent contents leads to a lower Rfree due to a kind of
 solvent flattening effect. Of course, if a significant part of the
 molecule(s) is/are disordered, this will lead to a degradation of the
 Rfree. 
 
 My 2 cents,
 Herman

Re: [ccp4bb] how to remove part of data with bad signal to noise ratio

[Clement Angkawidjaja]

Dear Herman,

You are right. Thank you for the explanation.

Clement

 Dear Clement,

 In case of a noisy experimental map, you have to do explicit solvent
 flattening. However, in case of molecular replacement, if the model
 occupies only say 30% of the asymmetric unit, the solvent where there is
 no model, will be flattened automatically. You can also view it like
 this: if 70% of the asymmetric unit is featureless solvent, the model at
 hand (=flat bulk solvent model), will be very accurate. I never really
 tested this, but in the cases where I had a very high solvent content, I
 was always surprised by the quality of the electron density maps. Off
 course, crystals with a high solvent content tend to diffract poorly and
 if the solvent is not featureless, this will not work either.

 If you get high Rfree values for a structure with high solvent content,
 I would get suspicious and look for extra molecule(s), which may have
 been overlooked. If these extra molecule(s) are disordered, this will
 off course lead to high Rfree values.

 Best,
 Herman

 -Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
 Clement Angkawidjaja
 Sent: Tuesday, May 24, 2011 11:19 AM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] how to remove part of data with bad signal to
 noise ratio

 But you have to do solvent flattening (density modification), which
 people often (unintentionally?) skip for structures solved with
 molecular replacement. Please correct me if I am wrong.

 Clement

 On May 24, 2011, at 6:01 PM, herman.schreu...@sanofi-aventis.com wrote:

 This is not my experience. Provided the solvent is featureless, I find

 that a high solvent contents leads to a lower Rfree due to a kind of
 solvent flattening effect. Of course, if a significant part of the
 molecule(s) is/are disordered, this will lead to a degradation of the
 Rfree.

 My 2 cents,
 Herman

Re: [ccp4bb] image file extensions

[Clement Angkawidjaja]

.ipf if you have files from (old) image plate detectors.

clement

 Dear all,

 I'm trying to create some space on our server and want to compress all
 x-ray data files.  I'm wondering what extensions I should search for.
 mccd and img come to mind easily.  What other extensions are commonly
 used?

 Thanks.


 Andreas



 --
  Andreas F#65533;ster, Research Associate
  Paul Freemont  Xiaodong Zhang Labs
 Department of Biochemistry, Imperial College London
  http://www.msf.bio.ic.ac.uk



Clement Angkawidjaja, Ph.D
Specially appointed assistant professor
Laboratory of Molecular Biotechnology (Kanaya Lab)
Division of Advanced Science and Biotechnology
Graduate School of Engineering, Osaka University
2-1 Yamadaoka, Suita-shi, Osaka 565-0871
Japan

Re: [ccp4bb] Question on calculation of RMSD

[Clement Angkawidjaja]

The lowest rmsd might not be the biological relevant one 
True, however the least square fit using the right residues (thus producing the 
lowest rmsd possible) can really tell you the most significant differences (or 
not signifcant ones) that cause biological changes. Human eyes are often not 
good in doing this. Using automated lsq fit programs can give you precise 
(initial) information using the lowest human effort and low chance of human 
error.

Clement

As confucius would say, don't trust the output of a program if you have not 
programmed it yourself or know what it's doing.

Last words of wisdom for tonight.

Jürgen

-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://web.mac.com/bosch_lab/

On Nov 14, 2010, at 8:32 PM, Clement Angkawidjaja wrote:


  DALI server (http://ekhidna.biocenter.helsinki.fi/dali_server/). Choose the 
  pairwise alignment function. It is all automatic and will give you the 
  lowest rmsd. Note, however, that it will omit parts that are very different 
  for calculation.

  Within CCP4, SUPERPOSE or COOT can also do that. You need to specify the 
  residues you want to use for calculation for the lsq fit function.

  Regards,
  Clement Angkawidjaja, PhD
  Specially Appointed CMP Assistant Professor
  Graduate School of Engineering
  Osaka University
  2-1 Yamadaoka GSE Commoon East 8F
  Suita-shi, Osaka 565-0871, Japan
  Tel/Fax +81-6-6879-4580
  http://www.mls.eng.osaka-u.ac.jp/~bio_ext/mlsbe123/clement.html
  ///
  G30 Chemistry/Biology Combined Major Program
  http://cmp.sci.osaka-u.ac.jp/CMP/

  -Original Message- 
  From: E rajakumar
  Sent: Monday, November 15, 2010 6:52 AM
  To: CCP4BB@JISCMAIL.AC.UK
  Subject: [ccp4bb] Question on calculation of RMSD

  Dear All
  I have two structures of homo-dimeric protein complex with different DNA.
  I want to calculate RMS deviation between second monomer from these two 
  complexes by fixing superposed first monomer.

  This I require to know what is the effect of DNA on relative orientation of 
  two monomers in the dimer.

  Previously I was using MOLEMAN2 to do this calculation.

  Please can you suggest me any other program to do this calculation.

  Thanking you
  Raj


  E. Rajakumara
  Postdoctoral Fellow  Strcutural Biology Program  Memorial Sloan-Kettering 
  Cancer Center  New York-10021  NY  001 212 639 7986 (Lab)  001 917 674 6266 
  (Mobile)

Re: [ccp4bb] how to optimize small rod-shaped crystals

[Clement Angkawidjaja]

I strongly agree with Eric Larson’s suggestion on trying to see the diffraction 
of your crystal. The most straightforward solution. Other suggestions may work 
too, but there are chances they will still give you false positives.

If you need bigger crystals, try to slow down the nucleation (use lower 
temperature, different ratio of protein:crystallant, etc).

Clement

From: yybbll 
Sent: Wednesday, November 17, 2010 2:42 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] how to optimize small rod-shaped crystals

Hi, everybody,

I try to crystallize one membrane protein. All crystals were grown by 
handing-drop vapor diffusion at 20 degree. A protein solution containing about 
8-10mg/ml protein in 20mM Tris (pH7.5), 0.017% DDM, 100mM NaCl, 10% glycerol, 
2mM DDT was mixed with an equal volume of a reservoir solution containing 45% 
PEG200, 0.1 M phosphate/citrate (pH4.2). First crystal appeared in the drop 
within 4 days. And one week a lot of crystals appeared in the drops.

Our question is all of these crystals are too small to check them by X-ray 
diffraction and SDS-PAGE. We are not sure they are protein crystals or salt 
crystals. Our condition seems difficult to produce salt crystal. But I am a 
little warry because we use reloaded our sample to small Ni-resin column to 
reduce the concentration of detergent. Maybe some nickel ion dropped off, and 
then our protein sample contained some this ion. And nickel ion may react with 
phosphate, and then produced nickel phosphate crystal. Could somebody tell me 
if it is possible? 

I attach some photos of our crystals. Could somebody give me some suggestions 
about how to optimize this type crystal to get bigger crystal?

Thanks a lot!

Yibin

Re: [ccp4bb] Question on calculation of RMSD

[Clement Angkawidjaja]

DALI server (http://ekhidna.biocenter.helsinki.fi/dali_server/). Choose the 
pairwise alignment function. It is all automatic and will give you the 
lowest rmsd. Note, however, that it will omit parts that are very different 
for calculation.


Within CCP4, SUPERPOSE or COOT can also do that. You need to specify the 
residues you want to use for calculation for the lsq fit function.


Regards,
Clement Angkawidjaja, PhD
Specially Appointed CMP Assistant Professor
Graduate School of Engineering
Osaka University
2-1 Yamadaoka GSE Commoon East 8F
Suita-shi, Osaka 565-0871, Japan
Tel/Fax +81-6-6879-4580
http://www.mls.eng.osaka-u.ac.jp/~bio_ext/mlsbe123/clement.html
///
G30 Chemistry/Biology Combined Major Program
http://cmp.sci.osaka-u.ac.jp/CMP/

-Original Message- 
From: E rajakumar

Sent: Monday, November 15, 2010 6:52 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Question on calculation of RMSD

Dear All
I have two structures of homo-dimeric protein complex with different DNA.
I want to calculate RMS deviation between second monomer from these two 
complexes by fixing superposed first monomer.


This I require to know what is the effect of DNA on relative orientation of 
two monomers in the dimer.


Previously I was using MOLEMAN2 to do this calculation.

Please can you suggest me any other program to do this calculation.

Thanking you
Raj


E. Rajakumara
Postdoctoral Fellow  Strcutural Biology Program  Memorial Sloan-Kettering 
Cancer Center  New York-10021  NY  001 212 639 7986 (Lab)  001 917 674 6266 
(Mobile)