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Hiya Mark once again I find myself asking why not give the authors deposited file alongside any other 'cleaned-up' PDB files. The authors' one could be foo.pdb_0 then after PDB heterogen annotation you get foo.pdb_1 - if the heterogens are subsequently handled differently then you could have foo.pdb_2 for the 'remediated' file. This latter has certainly happened as there appear to be 'orphan' heterogen definitions in the pdb that are not currently used by any entries - most likely these were 'split' when atoms were taken out and associated with polymer entities, or in some cases, I notice, 'lumped' when they have been included with residues alongside to give a new larger heterogen. PDB file versioning would also give transparency in cases such as occupancy remediation when the pdb altered all occupancies that summed to >1.0 to enforce a total of 1.0 (giving holes in the authors' density presumably) which may mystify the sharp-eyed user. Currently there are the REV_DAT lines in the header but these give only the titles of changed cards not any detailed explanation. Likewise REVDAT only starts at foo.pdb_1 in my example - still missing the authors original intent. all the best Martyn ________________________________ From: Mark J van Raaij <[log in to unmask]> To: [log in to unmask] Sent: Tuesday, 9 July 2013, 15:23 Subject: Re: [ccp4bb] modified amino acids in the PDB - really the only complicated case would be where a group is covalently linked to more than one amino acid, wouldn't it? Any case where only one covalent link with an is present could (should?) be treated as a special amino acid, i.e. like selenomethionine. - groups without any covalent links to the protein are better kept separate I would think (but I guess this is stating the obvious). Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 9 Jul 2013, at 12:49, Frances C. Bernstein wrote: > In trying to formulate a suggested policy on het groups > versus modified side chains one needs to think about the > various cases that have arisen. > > Perhaps the earliest one I can think of is a heme group. > One could view it as a very large decoration on a side > chain but, as everyone knows, one heme group makes four > links to residues. In the early days of the PDB we decided > that heme "obviously" had to be represented as a separate group. > > I would also point out that nobody would seriously suggest that > selenomethionine should be represented as a methionine with a > missing sulfur and a selenium het group bound to it. > > Unfortunately all the cases that fall between selenomethionine > and heme are more difficult. Perhaps the best that one must > hope for is that whichever representation is chosen for a > particular case, it be consistent across all entries. > > Frances > > P.S. One can also have similar discussions about the representation > of microheterogeneity and of sugar chains but we should leave those > for another day. > > ===================================================== > **** Bernstein + Sons > * * Information Systems Consultants > **** 5 Brewster Lane, Bellport, NY 11713-2803 > * * *** > **** * Frances C. Bernstein > * *** [log in to unmask] > *** * > * *** 1-631-286-1339 FAX: 1-631-286-1999 > ===================================================== > > On Tue, 9 Jul 2013, MARTYN SYMMONS wrote: > >> Hi Clemens >> I guess the reason you say 'arbitrary' is because there is no explanation of this >> rule decision? >> It would be nice if some rationalization was available alongside the values given. >> So a sentence along the lines of 'we set the number owing to the following >> considerations' ? >> However a further layer of variation is that the rule does not seem to be >> consistently applied >> - just browsing CYS modifications: >> iodoacetamide treatment gives a CYS with only 4 additional atoms but it is split >> off as ACM. >> However some ligands much larger than 10 residues have been kept with the cysteine >> ( for example CY7 in 2jiv and NPH in 1a18. >> My betting is that it depends on whether something has been seen 'going solo' as a >> non-covalent ligand previously so that it pops up as an atomic structural match with >> a pre-defined three-letter code. >> This would explain for example the ACM case which you might expect to occur in a >> modified Cys. But it has also been observed as a non-polymer ligand in its own right >> so goes on as a separate modification? >> However to be honest I am not sure I have ever seen the rationale for this written >> down. >> 'Non-polymer' heterogens can turn up either linked or not. Once they are in the >> residues they have to make a call on which kind of backbone they will feature in >> within the pdb. >> That is why there is 'D5M' for non-polymer deoxyAMP. Also known as ' DA' when it >> is 'DNA-linking' but so far not fessing up to life under a third code as >> 'RNA-linking'.... >> Now is perhaps the time to ask for explanations of these nomenclature features before >> they become hard-wired in the new pdb deposition system (however there may be time - >> I refer you to my previous posting ;). >> >> Cheers >> Martyn >> >> Dr Martyn Symmons >> Cambridge >> _____________________________________________________________________________________ >> From: Michael Weyand <[log in to unmask]> >> To: [log in to unmask] >> Sent: Monday, 8 July 2013, 10:03 >> Subject: [ccp4bb] modified amino acids in the PDB >> Dear colleagues, >> We deposited protein structures with modified lysine side chains and >> were surprised that the PDB treats the modification as an independent >> molecule, with a ?LINK? record indicating the covalent bond ? instead of >> defining a modified residue (that?s what we had uploaded to the PDB). >> Apparently, anything attached to an amino acid is considered an >> independent molecule (and the lysine just called a regular lysine) if it >> comprises more than 10 atoms (see below for the PDB guidelines). >> I think that?s kind of arbitrary and would give all modified residue >> also modified names ? i.e. individual names for all modified lysines, as >> it is done for acetyl- or methyl-lysines, for example. I wonder what >> other people?s opinion is?! >> Best regards >> Clemens >> ------------------------------------------------------------------------------------ >> ------------ >> This is in accordance to the wwPDB annotation guidelines >> (http://www.wwpdb.org/procedure.html#toc_2). >> "*Modified amino acids and nucleotides* If an amino acid or nucleotide >> is modified by a chemical group greater than 10 atoms, the residue will >> be split into two groups: the amino acid/nucleotide group and the >> modification. A link record will be generated between the amino >> acid/nucleotide group and the modification. For modified amino acids and >> nucleotides that were not split will follow standard atom nomenclature."