Re: [ccp4bb] Database for submitting unprocessed diffraction data

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

Re: [ccp4bb] Crystallization Robots

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

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

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

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

ess 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

[ccp4bb] Strategies for increasing Trp content of proteins

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

[ccp4bb] MizzouForward faculty hiring campaign

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

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

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,

[ccp4bb] Design of SUMO fusion proteins

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.

Re: [ccp4bb] unknown density

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] Tiny rocks on my CX100 shipping dewar

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

[ccp4bb] Tenure track faculty position University of Missouri

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

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

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

Re: [ccp4bb] Covalent Cysteine Aduct

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:

Re: [ccp4bb] Flexible C terminus

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

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

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,

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

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

Re: [ccp4bb] difficult molecular replacement solution

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

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

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

Re: [ccp4bb] Changes in quaternary structure

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

Re: [ccp4bb] COOT crashes when I merge molecules

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:

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

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.

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

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

Re: [ccp4bb] covalent bond

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

Re: [ccp4bb] A challenging Molecular replacement

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

Re: [ccp4bb] Incorrect Structure in the PDB

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

Re: [ccp4bb] Incorrect Structure in the PDB

/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 Depa

Re: [ccp4bb] Incorrect Structure in the PDB

/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 Depa

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

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

Re: [ccp4bb] Structure comparison

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

[ccp4bb] Request for session proposals for ACA Toronto 2018

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

Re: [ccp4bb] RMSD plot

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. >

Re: [ccp4bb] For stabilizing protein-protein complex

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

Re: [ccp4bb] handling crystals in volatile solvents

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

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

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

Re: [ccp4bb] Thin plate crystals

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

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

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

Re: [ccp4bb] asymmetric homotrimer in the asu

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

Re: [ccp4bb] Phenix refinement

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

Re: [ccp4bb] Phenix refinement

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

Re: [ccp4bb] modeling flexible ends on proteins

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)

Re: [ccp4bb] Merge PDB chains

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

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

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

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

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

[ccp4bb] Aggregation assay

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

Re: [ccp4bb] suggestions for cryoprotectant

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

Re: [ccp4bb] Best compounds for heavy atom soaks

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

Re: [ccp4bb] DNA Protein co- Crystallization

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

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

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.

[ccp4bb] molprobity

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

Re: [ccp4bb] SA-omit map

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

Re: [ccp4bb] Problematic PDBs

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

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

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

Re: [ccp4bb] Crystallization condition for trimeric protein

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

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

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

Re: [ccp4bb] cryo condition

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

Re: [ccp4bb] pKa and electrostatic affinity

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

[ccp4bb] predicting membrane-association domain

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

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

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

Re: [ccp4bb] Heterotetrameric protein

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

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

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:

Re: [ccp4bb] how can merge two PDB

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.

Re: [ccp4bb] Low resolution structure determination advice

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

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

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

Re: [ccp4bb] relationship between B factors and Koff

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

[ccp4bb] Fill map/mask with dummy atoms?

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

[ccp4bb] Off-topic: hollow protein crystals

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.

Re: [ccp4bb] Possible sulphate

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]

[ccp4bb] Retraction of 12 Structures

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:

[ccp4bb] Mounting needle-shaped crystals

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