I had thought that after discussion on this bulletin board we could find no rational scientific reason why the PDB renumbers waters from the N to the C term of the polypeptides (and 5' to 3' of nucleic chains?). https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1311&L=CCP4BB&D=0&P=12314
I think that provided you follow the agreed rules on chain ids (see below) then you have a 'right of veto' on the water renumbering. You also have a 'right of veto' for the water movement to symmetry-related positions - which would involve chain id change. So probably the best way is to assign the chain ids yourself and just say you don't want any of your waters renumbered. Then keep track of them yourself as Ed suggested using documented community tools. One related question is how waters with alternate positions are dealt with. I cannot find clear documentation on this. Often sidechains with alternate positions motivate alternate waters during refinement. But I believe these are removed during the deposition water renumbering step. So if you have particular waters in alternative positions - say owing to a Michaelis complex at the active site - then the renumbering will likely split your water in alternate positions to produce two apparently unrelated, differently-numbered, solvent atoms. It could be argued how can you know these are alt pos of the same water? But if you have refined them like that then it is good for users of your coordinates to see that documented. It may be that the new PDB Deposition System is more flexible in this regard - I have not used it yet. Below is the current agreed procedure from the wwPDB website. Hope that helps. regards Martyn How are chain IDs assigned to chemical groups and waters? All chemical groups and waters within 5 Ångstroms of any atom of a polymeric chain will be considered to be associated with that chain and will be assigned the same chain ID as that polymer. If a particular chemical group/water is equidistant from more than one chain, then the chain ID is randomly assigned to be that of any one of these polymers. Waters further than 5 Ångstroms away from the polymer that can be moved by symmetry to within 5 Ångstroms, will then be automatically moved and the author will be notified. If there are objections, the waters will be moved back to their original positions. Waters further than 5 Ångstroms away from any polymer, which cannot be brought closer to a polymer chain by application of symmetry, will be brought to the attention of the depositor. The waters will be listed in REMARK 525 with the distance to the nearest macromolecule listed. Authors will be given the opportunity to remove the waters or update the coordinates. Authors may choose to retain the distant waters in the entry. ________________________________ From: Edward A. Berry <[email protected]> To: [email protected] Sent: Monday, 7 April 2014, 15:25 Subject: Re: [ccp4bb] Renumbering of water molecules during deposition After deposition (my experience is with RCSB) you will get back a processed file to verify. See how the waters have been renumbered, and renumber in such a a way that your original scheme is easily identifiable but in keeping with whatever the renumbering was trying to achieve- e.g. your waters X1,X2,X3 could become A1001, A1002, A1003 and the symmetry related waters B1001, B1002, B1003. Discuss with the annotator to see how your waters can be renumbered in a recognizable way in keeping with requirements of the PDB conventions. Then in future depositions keep this same scheme (you may still need to renumber the original processed file each time). eab Eckhard Hofmann wrote: > Hi all, > during deposition of structures the water numbering is frequently changed. > I would love to keep specific numbers for critical water molecules e.g. > in an active site in related proteins (mutants, ligand soaks), to > facilitate easier discussion in a manuscript. > > Is there a general agreement how to treat these? > > One way to deal with this is would be to use an arbitrary offset: > A1-A233 protein > A301 ligand > A302 another ligand > A401-404 4 special waters > A500- general solvent > > Any input welcome ;-) > All the best, > Eckhard > -- > Prof. Dr. Eckhard Hofmann <[email protected]> > Ruhr-Uni Bochum > AG Proteinkristallographie, LS Biophysik, ND04/318 > 44780 Bochum > Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762 >
