[ccp4bb] Table in NSMB
Dear all, I'm filling out my table for NSMB, about a structure of protein ligand bound to a receptor. They ask for 3 different lines regarding number of atoms bfactor. 1) Protein 2) Ligand/Ion 3) Water. Does my protein ligand belong to Protein or Ligand/Ion? Thanks,
Re: [ccp4bb] Table in NSMB
On Tue, Feb 18, 2014 at 8:19 AM, Jan van Agthoven janc...@gmail.com wrote: I'm filling out my table for NSMB, about a structure of protein ligand bound to a receptor. They ask for 3 different lines regarding number of atoms bfactor. 1) Protein 2) Ligand/Ion 3) Water. Does my protein ligand belong to Protein or Ligand/Ion? Why not list them each explicitly? In my experience the recommended table of crystallography statistics for most journals is just a suggestion, not a strict format. If you leave out information they might complain, but surely they won't object if you include additional details. (They usually just exile it to the unformatted supplementary materials anyway.) -Nat
Re: [ccp4bb] Table in NSMB
Hi Jan - I believe that ligand in this case refers to small molecule ligands, e.g. ATP or NADPH. If your ligand is a protein or even a peptide, I think it belongs in the protein category. (Thus, you may have no ligand atoms, unless you have bound sulfate, PEG, etc.) - Matt On 2/18/14 11:19 AM, Jan van Agthoven wrote: Dear all, I'm filling out my table for NSMB, about a structure of protein ligand bound to a receptor. They ask for 3 different lines regarding number of atoms bfactor. 1) Protein 2) Ligand/Ion 3) Water. Does my protein ligand belong to Protein or Ligand/Ion? Thanks, -- 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] Table in NSMB
I would have thought that ligands are ligand/ion?. What I have just done with a recent structure and I await the reviewers noticing or not is include the ethylene glycol from the cryo that I can (probably) see in a solvent (rather than water) atom number and bfactor line along with water (which probably includes sodium/chloride ions etc misassigned as water) rather than as ligand. I would suggest that Protein, Ligand, Solvent/Ion is probably a better break down than Protein, Ligand/Ion and Water alhtough if I had an ion associated with a ligand Mg on my ATP I would have that in ligand rather than ion. What then should you do if there are waters then visible on the ion??? I guess the question that this is really asking is whether the Bfactor of what you are describing as a significant ligand in your discussion is well ordered compared to the surrounding protein. Gubbins filling out density peaks in the solvent area probably should not be included in that line. Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
Re: [ccp4bb] Table in NSMB
Sorry misread the initial post. Yes a protein ligand should be in the protein but you could give B factor number for each chain- my comments about what goes in ligand and what in solvent may be of general interest/comment Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
[ccp4bb] AW: [ccp4bb] Table in NSMB
If the ligand is a bona fide protein (more than a few amino acids and its own stable fold), I would include it under protein. However it is a matter of taste and, as Nat says, it will probably be dumped in the supplementary materials to be never looked at again. Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Nat Echols Gesendet: Dienstag, 18. Februar 2014 17:29 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Table in NSMB On Tue, Feb 18, 2014 at 8:19 AM, Jan van Agthoven janc...@gmail.commailto:janc...@gmail.com wrote: I'm filling out my table for NSMB, about a structure of protein ligand bound to a receptor. They ask for 3 different lines regarding number of atoms bfactor. 1) Protein 2) Ligand/Ion 3) Water. Does my protein ligand belong to Protein or Ligand/Ion? Why not list them each explicitly? In my experience the recommended table of crystallography statistics for most journals is just a suggestion, not a strict format. If you leave out information they might complain, but surely they won't object if you include additional details. (They usually just exile it to the unformatted supplementary materials anyway.) -Nat
Re: [ccp4bb] AW: [ccp4bb] Table in NSMB
Thanks for all responses, Yes I'll keep my ligand in the protein section, and will add extra information regarding the ligand/receptor. They actually asked for separate b-factors during review, so I guess they'll be willing to see it in the final table. Jan 2014-02-18 11:39 UTC-05:00, herman.schreu...@sanofi.com herman.schreu...@sanofi.com: If the ligand is a bona fide protein (more than a few amino acids and its own stable fold), I would include it under protein. However it is a matter of taste and, as Nat says, it will probably be dumped in the supplementary materials to be never looked at again. Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Nat Echols Gesendet: Dienstag, 18. Februar 2014 17:29 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Table in NSMB On Tue, Feb 18, 2014 at 8:19 AM, Jan van Agthoven janc...@gmail.commailto:janc...@gmail.com wrote: I'm filling out my table for NSMB, about a structure of protein ligand bound to a receptor. They ask for 3 different lines regarding number of atoms bfactor. 1) Protein 2) Ligand/Ion 3) Water. Does my protein ligand belong to Protein or Ligand/Ion? Why not list them each explicitly? In my experience the recommended table of crystallography statistics for most journals is just a suggestion, not a strict format. If you leave out information they might complain, but surely they won't object if you include additional details. (They usually just exile it to the unformatted supplementary materials anyway.) -Nat
