Re: [ccp4bb] [Fwd: Re: [ccp4bb] FW: New ligand 3-letter code (help-7071)]
Hi Ben From discussions we have had with PDBe they consider tautomers to be different compounds (just as stereoisomers would be considered to be different compounds), since they require different restraint dictionaries, so each tautomer that was observed would require a unique 3-lettter code. Of course you still have to have evidence (e.g. from the H-bonding pattern) that what you are really seeing are different tautomers, but that's a different question. Cheers -- Ian On 24 June 2015 at 12:50, Ben Bax benjamin.d@gsk.com wrote: Another major problem with the PDB is that it does not seem to believe in the existence of different tautomers or protonation states. For example the ATP analogue AMPPNP can have the nitrogen between the beta and gamma phosphates protonated (-P-NH-P) or unprotonated (P-N=P), and there are well documented examples of both tautomers in the PDB (NH being a hydrogen bond donor and N a hydrogen bond acceptor). If you look in the CSD you can see that the protonation state of the nitrogen changes the geometry of the P-N-P bond. However, as I understand it, the PDB considers all tautomeric (and protonated) forms of AMPPNP the same. When I tried to deposit a specific AMPPNP tautomer in 2013, they would not accept it. The PDB also seems to believe, as I understand it, that the overall charge on AMPPNP is zero and that the phosphates do not carry negative charge. *Ben Bax* *Senior Scientific Investigator* BioMolecular Sciences UK RD Platform Technology Science *GSK* *Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK* *Email **benjamin.d@gsk.com* benjamin.d@gsk.com *Mobile +44 (*0) 7912 600604 *Tel +*44 (0) 1438 55 1156 *gsk.com* http://www.gsk.com/ | *Twitter* http://twitter.com/GSK | *YouTube* http://www.youtube.com/user/gskvision | *Facebook* http://www.facebook.com/glaxosmithkline | *Flickr* http://www.flickr.com/photos/glaxosmithkline -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UK] On Behalf Of Martyn Symmons Sent: 22 June 2015 23:39 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] [Fwd: Re: [ccp4bb] FW: New ligand 3-letter code (help-7071)] Well the problem is there is a lot more to a ligand than PDB coordinates - little things like bond orders... In addition people can publish ligands with atoms for which they have no density - so zero-occupancy is allowed too. So who should get priority - the group who publishes a ligand first, or the ones who actually have density for all the atoms? These sorts of complications mean we all benefit from peer-review of the structure - that is why we put things on hold. And authors should have a chance to change their ligand definition based on reviewers' comments - just as they are allowed to improve the PDB coordinates. So it is a worry for them that the PDB might 'publish' the ligand aspect of their work before they have completed the peer-review process. Maybe you don't believe is peer-review - in reply to which I'd paraphrase what people say about democracy - it's pretty bad but better than the alternatives. But to return to the point I made: what really is the problem with maintaining and modifying _separate_ definitions with authors' _separate_ deposited coordinates (and bond orders) while structures are on hold and being reviewed? Journals manage to keep all those submitted papers separate in their databases. cheers M. On Mon, Jun 22, 2015 at 3:12 AM, Edward A. Berry ber...@upstate.edu wrote: I can't imagine a journal doing that can you? When I work on my supplementary material in a paper I don't expect that the journal will take a bit out and publish it separately to support the work of my competitors. Not out of spite that I was beaten - but because I don't want to take the responsibility for checking their science for them! I don't see the problem here. What about the dozens of authors who will benefit from using your ligand in their structure _after_ your structure comes out? You don't take responsibility for checking their science. Every author gets a copy of his final structure to check before it is released and each is responsible for his own. The only difference here is whether the competitor got to use it first, (which might sting a bit) or only after you had already made it your own with the first structure. I guess the ligand database is the responsibility of the pdb, but they depend on first depositors to help set up each ligand, so it is not surprising if the type model has coordinates from the first depositor's structure (although it would be convenient if they were all moved to c.o.m. at 0,0,0). When another group publishes a structure with the ligand, they will not be publishing the first depositor's coordinates because the ligand will be moved to its position in their structure and refined
[ccp4bb] Last 2 updates - aimless and scala
Hi folkd, We have just collected some data and was busy processing and ran aimless having updated to the latest versions (upgrades 10 and 11 I think). Both aimless and then scala stops/fails almost immediately without writing any log files etc. I tried running the same unmerged mtz on an older version and it runs fine. Is this a bug? J _ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293
Re: [ccp4bb] [Fwd: Re: [ccp4bb] FW: New ligand 3-letter code (help-7071)]
Another major problem with the PDB is that it does not seem to believe in the existence of different tautomers or protonation states. For example the ATP analogue AMPPNP can have the nitrogen between the beta and gamma phosphates protonated (-P-NH-P) or unprotonated (P-N=P), and there are well documented examples of both tautomers in the PDB (NH being a hydrogen bond donor and N a hydrogen bond acceptor). If you look in the CSD you can see that the protonation state of the nitrogen changes the geometry of the P-N-P bond. However, as I understand it, the PDB considers all tautomeric (and protonated) forms of AMPPNP the same. When I tried to deposit a specific AMPPNP tautomer in 2013, they would not accept it. The PDB also seems to believe, as I understand it, that the overall charge on AMPPNP is zero and that the phosphates do not carry negative charge. Ben Bax Senior Scientific Investigator BioMolecular Sciences UK RD Platform Technology Science GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK Email benjamin.d@gsk.commailto:benjamin.d@gsk.com Mobile +44 (0) 7912 600604 Tel +44 (0) 1438 55 1156 gsk.comhttp://www.gsk.com/ | Twitterhttp://twitter.com/GSK | YouTubehttp://www.youtube.com/user/gskvision | Facebookhttp://www.facebook.com/glaxosmithkline | Flickrhttp://www.flickr.com/photos/glaxosmithkline -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Martyn Symmons Sent: 22 June 2015 23:39 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] [Fwd: Re: [ccp4bb] FW: New ligand 3-letter code (help-7071)] Well the problem is there is a lot more to a ligand than PDB coordinates - little things like bond orders... In addition people can publish ligands with atoms for which they have no density - so zero-occupancy is allowed too. So who should get priority - the group who publishes a ligand first, or the ones who actually have density for all the atoms? These sorts of complications mean we all benefit from peer-review of the structure - that is why we put things on hold. And authors should have a chance to change their ligand definition based on reviewers' comments - just as they are allowed to improve the PDB coordinates. So it is a worry for them that the PDB might 'publish' the ligand aspect of their work before they have completed the peer-review process. Maybe you don't believe is peer-review - in reply to which I'd paraphrase what people say about democracy - it's pretty bad but better than the alternatives. But to return to the point I made: what really is the problem with maintaining and modifying _separate_ definitions with authors' _separate_ deposited coordinates (and bond orders) while structures are on hold and being reviewed? Journals manage to keep all those submitted papers separate in their databases. cheers M. On Mon, Jun 22, 2015 at 3:12 AM, Edward A. Berry ber...@upstate.edumailto:ber...@upstate.edu wrote: I can't imagine a journal doing that can you? When I work on my supplementary material in a paper I don't expect that the journal will take a bit out and publish it separately to support the work of my competitors. Not out of spite that I was beaten - but because I don't want to take the responsibility for checking their science for them! I don't see the problem here. What about the dozens of authors who will benefit from using your ligand in their structure _after_ your structure comes out? You don't take responsibility for checking their science. Every author gets a copy of his final structure to check before it is released and each is responsible for his own. The only difference here is whether the competitor got to use it first, (which might sting a bit) or only after you had already made it your own with the first structure. I guess the ligand database is the responsibility of the pdb, but they depend on first depositors to help set up each ligand, so it is not surprising if the type model has coordinates from the first depositor's structure (although it would be convenient if they were all moved to c.o.m. at 0,0,0). When another group publishes a structure with the ligand, they will not be publishing the first depositor's coordinates because the ligand will be moved to its position in their structure and refined against their data, probably with somewhat different restraints. If the ligand is a top secret novel drug lead that your company is developing I guess it would come as a shock to find someone else has already deposited it, and it might be good to hasten not the publication but protecting of the compound with a patent! Although Miriam says a new 3-letter code is generated when no match is found, I believe the depositor's code will be used if it is available, at least one of mine was last year, so there is some use for Nigel's utility if you want to stamp your new compound with a rememberable name. eab
Re: [ccp4bb] Last 2 updates - aimless and scala
It's hard to know without more information. If there really is no log file, then that suggests the job hasn't even started, so maybe something wrong with the ccp4i interface Which task were you using? 1. Symmetry, Scale, Merge (Aimless), the recommended one, or 2. Find Symmetry, Scale and Merge (Scala), the old one Are you sure there is no log file? Do the programs start from the command line, e.g. type pointless? For what it's worth, it's all working for me Phil On 24 Jun 2015, at 11:27, Joel Tyndall joel.tynd...@otago.ac.nz wrote: Hi folkd, We have just collected some data and was busy processing and ran aimless having updated to the latest versions (upgrades 10 and 11 I think). Both aimless and then scala stops/fails almost immediately without writing any log files etc. I tried running the same unmerged mtz on an older version and it runs fine. Is this a bug? J _ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293
[ccp4bb] Several postdoctoral positions (max 9) at Umeå University, Sweden
Please note the opening for post-doctor positions at UCMR, Umeå University. Best wishes Elisabeth Sauer-Eriksson - Postdoctoral Research Opportunities in Infection Biology and Molecular Infection Medicine at Umeå University, Sweden Deadline: August 17, 2015 Several positions are open for postdoctoral candidates interested to do research in the highly interactive and multidisciplinary research environment UCMR – Umeå Centre for Microbial Research at Umeå University, Swedenhttp://www.ucmr.umu.se. UCMR includes The Laboratory for Molecular Infection Medicine Sweden (MIMS) http://www.mims.umu.se – the Swedish node of The Nordic EMBL Partnership for Molecular Medicine. UCMR-MIMS researchers combine a strong molecular infection biology programme with chemical biology to clarify molecular mechanisms of microbial infections. We aim to recruit new postdoctoral scientists with competence and ideas that will strengthen the research environment and contribute to its renewal. The programme is open to all nationalities and features of the positions include: • Development of a project proposal forms the basis for recruitment • Funding for research within a multidisciplinary environment • Two years of secure funding • Access to UCMR-MIMS-affiliated core facilities and technical platforms. The positions are full-time for 24 months. Applicants should have a PhD degree in a field relevant for the position preferably completed within the past three years. Candidates for the UCMR-MIMS postdoc programme are encouraged to consider one of the UCMR-MIMS project ideas listed below. The project idea should be developed into a research project proposal by the candidate. The PI of this project should be contacted for discussion and approval of eligibility before submission of the application to the Umeå University’s e-recruitment system Mynetwork (link below). The candidates' merits and project proposals will be assessed by a panel of UCMR researchers and a selected group of applicants will then be invited for on-line interviews. Thereafter it will be decided if some applicants will be offered a postdoctoral position. The number of positions that will be filled is not predetermined but can be a maximum of nine. Application The application should include: (i) a cover letter summarizing your qualifications and motives for the application; (ii) a short research proposal of approximately 2 pages describing a self-defined project based on one of the project ideas listed below; (iii) a Curriculum Vitae; (iv) a publication list; (v) copy of the official PhD degree certificate; (vi) the names and contact details of at least two references. For further information, please contact Professor Åke Forsberg, scientific secretary of UCMR and MIMS, +46-(0)90-785 2526, ake.forsberg[@]umu.se The application must be submitted electronically and all documents should be included in one single file in PDF format. You apply electronically through the e-recruitment system MyNetwork, click on the button below. We welcome your application! Project ideas: · Development of the next-generation force and bio-fluidic tools for cell adhesion characterisation, PI Magnus Anderssonhttp://www.mims.umu.se/images/postdoc_2015/Andersson_M.pdf · Mechanisms that control expression of the Helicobacter pylori inflammation associated SabA adhesion, PI Anna Arnqvisthttp://www.mims.umu.se/images/postdoc_2015/Arnqvist.pdf · Small molecule tools to study bacterial protein secretion, PI Mikael Elofssonhttp://www.mims.umu.se/images/postdoc_2015/Elofsson.pdf · RNA virus host – reservoir adaption. Genetic mechanisms and determinants, PI Magnus Evanderhttp://www.mims.umu.se/images/postdoc_2015/Evander.pdf · Global regulation of bacterial pathogenicity via sensors of envelope stress, PI Matthew Francishttp://www.mims.umu.se/images/postdoc_2015/Francis.pdf · Insight into the organization and function of bacterial cell walls and membranes by advanced NMR approaches, PI Gerhard Gröbnerhttp://www.mims.umu.se/images/postdoc_2015/Groebner.pdf · Bacterial sensing: Unraveling the role of 5’-untranslated RNAs for virulence factor expression, PI Jörgen Johanssonhttp://www.mims.umu.se/images/postdoc_2015/Johansson_J.pdf · Structure, assembly and spatial organization of bacterial cytoskeleton, PI Linda Sandbladhttp://www.mims.umu.se/images/postdoc_2015/Sandblad.pdf · Structural studies of proteins important for bacteria-host interactions, PI Elisabeth Sauer-Erikssonhttp://www.mims.umu.se/images/postdoc_2015/Sauer-Eriksson.pdf · Bacterial virulence mechanisms of the opportunistic pathogen Acinetobacter baumannii and the versatile pathogen Escherichia coli, PI Bernt Eric Uhlinhttp://www.mims.umu.se/images/postdoc_2015/Uhlin.pdf · Role of outer membrane vesicle (OMV)-associated bacterial
Re: [ccp4bb] [Fwd: Re: [ccp4bb] FW: New ligand 3-letter code (help-7071)]
Good afternoon both, there is also the issue of inconsistency of presentation. For example, Lysine, that is L-Lysine (LYS) is protonated on the side chain nitrogen (NZ), whiles as D-lysine (DLY) is not. i.e. you have NZ(HZ1, HZ2) for DLY, and NZ(HZ1, HZ2, HZ3) for LYS Miri On Wed, 2015-06-24 at 13:35 +0100, Ian Tickle wrote: Hi Ben From discussions we have had with PDBe they consider tautomers to be different compounds (just as stereoisomers would be considered to be different compounds), since they require different restraint dictionaries, so each tautomer that was observed would require a unique 3-lettter code. Of course you still have to have evidence (e.g. from the H-bonding pattern) that what you are really seeing are different tautomers, but that's a different question. Cheers -- Ian On 24 June 2015 at 12:50, Ben Bax benjamin.d@gsk.com wrote: Another major problem with the PDB is that it does not seem to believe in the existence of different tautomers or protonation states. For example the ATP analogue AMPPNP can have the nitrogen between the beta and gamma phosphates protonated (-P-NH-P) or unprotonated (P-N=P), and there are well documented examples of both tautomers in the PDB (NH being a hydrogen bond donor and N a hydrogen bond acceptor). If you look in the CSD you can see that the protonation state of the nitrogen changes the geometry of the P-N-P bond. However, as I understand it, the PDB considers all tautomeric (and protonated) forms of AMPPNP the same. When I tried to deposit a specific AMPPNP tautomer in 2013, they would not accept it. The PDB also seems to believe, as I understand it, that the overall charge on AMPPNP is zero and that the phosphates do not carry negative charge. Ben Bax Senior Scientific Investigator BioMolecular Sciences UK RD Platform Technology Science GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK Email benjamin.d@gsk.com Mobile +44 (0) 7912 600604 Tel +44 (0) 1438 55 1156 gsk.com | Twitter | YouTube | Facebook | Flickr -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Martyn Symmons Sent: 22 June 2015 23:39 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] [Fwd: Re: [ccp4bb] FW: New ligand 3-letter code (help-7071)] Well the problem is there is a lot more to a ligand than PDB coordinates - little things like bond orders... In addition people can publish ligands with atoms for which they have no density - so zero-occupancy is allowed too. So who should get priority - the group who publishes a ligand first, or the ones who actually have density for all the atoms? These sorts of complications mean we all benefit from peer-review of the structure - that is why we put things on hold. And authors should have a chance to change their ligand definition based on reviewers' comments - just as they are allowed to improve the PDB coordinates. So it is a worry for them that the PDB might 'publish' the ligand aspect of their work before they have completed the peer-review process. Maybe you don't believe is peer-review - in reply to which I'd paraphrase what people say about democracy - it's pretty bad but better than the alternatives. But to return to the point I made: what really is the problem with maintaining and modifying _separate_ definitions with authors' _separate_ deposited coordinates (and bond orders) while structures are on hold and being reviewed? Journals manage to keep all those submitted papers separate in their databases. cheers M. On Mon, Jun 22, 2015 at 3:12 AM, Edward A. Berry ber...@upstate.edu wrote: I can't imagine a journal doing that can you? When I work on my supplementary material in a paper I don't expect that the journal will take a bit out and publish it separately to support the work of my competitors. Not out of spite that I was beaten - but because I don't want to take the responsibility for checking their science for them! I don't see the problem here. What about the dozens of authors who
Re: [ccp4bb] references on application of broad specificity of enzyme
Hi Sreetama, It's very hard for anyone to help you out without more specific information. A quick google gets me a couple of potentially relevant hits: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3595323/ http://www.ncbi.nlm.nih.gov/pubmed/8650159 http://www.ncbi.nlm.nih.gov/pubmed/10218107 Shane Caldwell McGill On Tue, Jun 23, 2015 at 5:25 PM, sreetama das somon_...@yahoo.co.in wrote: Dear All, I have a transferase, which is showing broad specificity for both the substrates (nucleotides) in our organism of interest, but is highly specific in other organisms. Are there any references showing the applications of (bi-substrate) proteins with such broad specificity towards nucleotides? Thanking you, regards, Sreetama
[ccp4bb] Request
Hello BBians, sorry for the off-topic question. I have plasmid which possess the precision protease site to get rid of GST tag. Does anybody have precision protease plasmid. If someone has please share with me. I will be very thankful for you. Neeraj -- = Neeraj Kr. Mishra Department of Chemistry University of Minnesota Minneapolis, MN 55455 =
