[ccp4bb] Postdoctoral position at RCSB PDB San Diego

We are seeking a talented, highly motivated postdoctoral researcher to join the multidisciplinary team of the RCSB Protein Data Bank at UC San Diego, San Diego Supercomputer Center (SDSC). The successful applicant will work on research projects that drive next generation search tools at rcsb.org.

Re: [ccp4bb] Covalent Cysteine Aduct

Sorry, that was the wrong zenodo link! The correct one is: https://doi.org/10.5281/zenodo.220983 On Friday, 27 March 2020, 23:06:01 GMT, Jonathan Cooper <0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote: If you can model it as a lysine, it will be the beta-ME adduct. There's a

Re: [ccp4bb] Covalent Cysteine Aduct

If you can model it as a lysine, it will be the beta-ME adduct. There's a good one in 1b4e (see attached) which Eileen Jaffe pointed out to me and I never got round to sorting out. Now there's another one of 'mine' for which the data have not been deposited, but I did put the images on zenodo

Re: [ccp4bb] Covalent Cysteine Aduct

My guess would be that the chains were prepared under reducing conditions, mixed, and then allowed to oxidize. The surface adduct could easily form during this process. On Mar 27, 2020, at 4:38 PM, Cowan, Richard H. (Dr.) mailto:rc...@leicester.ac.uk>> wrote: Hi, The Fab constructs have a

Re: [ccp4bb] Covalent Cysteine Aduct

Hi Richard, Something that hasn’t been mentioned yet that might help settle the issue is to calculate an anomalous difference map with your I+, I- unmerged data. Even if you collect data far from the S edge, it is often possible to see positive anomalous difference density for S atoms in maps at

Re: [ccp4bb] Covalent Cysteine Aduct

There are several ways to prepare “Fabs”, using the term broadly. I would dig deeper in this case to be sure a thiol adduct isn’t possible. John > On Mar 27, 2020, at 5:38 PM, Cowan, Richard H. (Dr.) > wrote: > >  > Hi, > > The Fab constructs have a c-terminal cysteines on both the heavy

Re: [ccp4bb] Covalent Cysteine Aduct

Hi to All, Whilst this discussion has been going on, I've been carrying on with the work on this, and have now replaced the offending cysteine with CME. It seems to refine pretty well, fitting the density well, and the b-factors stay similar to those for nearby side chains, so I'm reasonably

Re: [ccp4bb] Covalent Cysteine Aduct

S-hydroxycysteine can cartainly show up under nonreducing storage or crystallization conditions, as an artifact. Cheers, Roger Rowlett On Fri, Mar 27, 2020, 5:45 PM Chris Fage wrote: > Hi Richard, > > I recently observed the sulfenic acid derivative of a cysteine residue > (S-hydroxy-Cys,

Re: [ccp4bb] Covalent Cysteine Aduct

I see. Might there be some discrepancy between best practice and what actually happened? ? On 27/03/2020 21:38, Cowan, Richard H. (Dr.) wrote: The Fab constructs have a c-terminal cysteines on both the heavy and light chains, which should form a disulphide. Adding reducing agent to the

Re: [ccp4bb] Covalent Cysteine Aduct

Hi Richard, I recently observed the sulfenic acid derivative of a cysteine residue (S-hydroxy-Cys, ligand ID CSO) in one of my high-resolution maps. Could it be possibly be this, H-bonded to a nearby water molecule? Best wishes, Chris On Fri, Mar 27, 2020 at 21:33 Paul Emsley wrote: > > On

Re: [ccp4bb] Covalent Cysteine Aduct

Hi, The Fab constructs have a c-terminal cysteines on both the heavy and light chains, which should form a disulphide. Adding reducing agent to the purification of the protein would potentially reduce this disulphide, possible causing issues the stability and heterogeneity? At least that's my

Re: [ccp4bb] Covalent Cysteine Aduct

On 27/03/2020 21:06, Cowan, Richard H. (Dr.) wrote: although [BME] seems unlikely, since the crystallized protein is a Fab. I don't follow. To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] Covalent Cysteine Aduct

Hi, The gene was synthesized for the expression construct, so a sequence error seems unlikely, but I'll check. There should be mass spec data on the purified protein, but our collaborators, who are also shut down for the moment, will have to get that for me, as well as sequence data. I don't

Re: [ccp4bb] Covalent Cysteine Aduct

Hi, The density is very much a linear chain, without side branches. That would lead me to discount a DTT adduct, since I can't see anywhere for the hydroxls to go? Thanks, Dr Richard Cowan Research Associate HWLSB 1/05 Department of Biochemistry University of Leicester Lancaster Road

Re: [ccp4bb] Covalent Cysteine Aduct

Looks like DTT adduct to me; but then again, if you did not have it, it probably is not. Petri Petri Kursula -- Professor -- Department of Biomedicine University of Bergen, Norway http://www.uib.no/en/rg/petrikursula petri.kurs...@uib.no -- Faculty of Biochemistry and

Re: [ccp4bb] Covalent Cysteine Aduct

Hi Robbie et al., I'm very sure on the crystallization conditions, but I'll check the purification for BME, although it seems unlikely, since the crystallized protein is a Fab. What I would be less sure on is the age of the reagents used. Is anyone aware of significant breakdown products

[ccp4bb] Open for COVID-19 Research for Structural Biology Data Collection

The SSRL Structural Biology beamlines 12-2, 9-2 and 4-2 and the Stanford-SLAC CryoEM facilities are open to user projects that are related to COVID-19 research. CryoEM Proposals may be submitted as service projects through our Stanford-SLAC Cryo-EM Center

Re: [ccp4bb] Covalent Cysteine Aduct

Are you absolutely sure about the conditions? The blob next to the sulfur looks pretty fat so I would guess BME.Cheers,RobbieOn 27 Mar 2020 21:32, "Cowan, Richard H. (Dr.)" wrote: Hi All, During the current enforced shutdown, I've been going back over some older data and spotted this in one

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] Raw diffraction images for SARS-CoV-2 related structures

HI This is great news. Can you let us at the PDB know the DOI's for each dataset so that we can associate the raw images with the PDB entry. We will be able to then show links to the raw images from PDB entry pages so that everyone can find them. Many thanks John John Berrisford PDBe +44 1223

[ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Dear all, It is a pleasure to be able to end the (GMT) week by calling for a huge round of applause for the Diamond team, who this afternoon started uploading a large collection of sets of raw diffraction images (77 as we write but the upload is still ongoing) for PDB entries that were

[ccp4bb] EM postdoc position at AstraZeneca UK

Dear all, I would like to remind you that we are still looking to fill a postdoc position at AstraZeneca (Cambridge UK) in collaboration with Prof Ashok Venkitaraman's group at the MRC Cancer Unit. This is an opportunity for a talented and self-motivated structural biologist to undertake

[ccp4bb] NSLS-II Update and Call for COVID-19 Rapid Access Proposals

A message from the NSLS-II Director Dear NSLS-II Users: On Monday, March 23, 2020, Brookhaven Lab transitioned to a state of minimum operations. The Lab is expected to operate in this mode until April 14, 2020, making further adjustments based on the evolving conditions. Only

Re: [ccp4bb] COVID-19 - help design protease inhibitors - 1st round Thurs midnight

27-Mar-2020 Rehovot Dear Frank Thanks very much for posting this msg - sounds just terrific and emphasizes just how important a role structural biology is playing to aid in the discovery of lead compounds for treatment of COVID-19, and how this is being done in a collaborative way

Re: [ccp4bb] COVID-19 - help design protease inhibitors - 1st round Thurs midnight

Hi Frank, Congratulations on this impressive and valuable contribution to the efforts against covid and I applaud your transparency and crowdsourcing efforts on this global problem. Your team is really an inspiration to us all. We are working to get all your structures uploaded for our med

Re: [ccp4bb] Ligand discrimination

Hi Nicolas, VHELIBS does a good job at that. Keep in mind though that the distinction between additives and functional molecules is done based on a list of compounds. There are compounds that can serve both as crystallisation agent and ligand in different contexts. Cheers, Robbie >

[ccp4bb] Ligand discrimination

Dear all, Could somebody point me to a good tool that providing a pdb id, could analyze its ligand(s) and distinguish between crystallographic agents and putative drugs. Many thanks in advance, Nicolas To unsubscribe

Re: [ccp4bb] Public resource for the structures, validation and re-modelling of Corona virus macromolecules

27-Mar-2020 13:40 Rehovot Dear Andrea, This looks like a terrific idea, We’ve just now added a pointer to the Public resource for the structures from beta-coronavirus with a focus on SARS-CoV and SARS-CoV-2 at the top of the section on "3D structural studies on Coronavirus COVID-19” on our

[ccp4bb] Public resource for the structures, validation and re-modelling of Corona virus macromolecules

Dear colleagues, we are methods developers in structural biology. During this time of crisis, we decided to put our brains to where our hearts are and have started a public resource for the structures from beta-coronavirus with a focus on SARS-CoV and SARS-CoV-2:

[ccp4bb] Rapid access for proprietary use of SPring-8 MX beamlines with mail-in service

Dear all, SPring-8, a Japan synchrotron facility, will resume user operation in next April after the scheduled shutdown. Currently, the shutdown due to COVID-19 is not under consideration. For those who wish to use synchrotron for proprietary research, SPring-8 is calling for rapid access