Hi Tristan, Wouter, Gert and everyone else, I hope that the sudden surge of zeal for eradication of error, re wrongly assigned cis peptides that involve non-proline residues, would not become too great to accept that there are exceptions. I agree, 3% in one entry is probably unjustified, and many reasons could be identified. But there were studies from as long ago as 1991 (Thornton et al), and 1998-1999 (Hilgnefeld et al) and others, where the question of non-proline cis peptides were investigated. A variety of lists were produced, and there are something like 86 (representative) entries with a genuine cis-peptide that is not involving a proline. The CISPEP record in a PDB entry notwithstanding, a map has to justify the assignment. Even when that is true, there ought to be a biological, or at least a biochemical, reason. Indeed there are, in two groups of proteins that I have been involved in, legume lectins and monocot lectins, but I won't go into the justification here. This message is just to emphasise that the crystallographers, the deposition service and the manuscript reviewers ought to be vigilant, to keep our databases clean and fit for purpose. So it is a collective responsibility, and I hope this is borne in mind as the discussion goes on.
Thanks for bringing this issue to the fore. Pierre Rizkallah From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Wouter Touw Sent: 16 February 2015 11:56 To: [email protected] Subject: Re: [ccp4bb] Cis-peptide bond checking Dear Tristan, Thank you for your post of earlier today regarding the problem of cis and trans peptide planes in the PDB. We also realised this problem a while ago and an article describing this problem and a solution is presently under review at Acta Cryst. D. After analysis of the PDB we can state with >95% certainty that ~4600 trans -> cis flips in ~2800 entries (and ~70K peptide-plane flips) are needed in the PDB. Around a third of the trans -> cis corrections concern non-prolines. We hope to be able to deal with the problem of cis -> trans corrections later. In the tradition of our group, the software to detect these flips is already available at swift.cmbi.ru.nl. Hopefully, the referees of our article consider this topic just as important as you and I do :-). Kind regards, Wouter Touw and Gert Vriend On 02/16/2015 10:58 AM, Tristan Croll wrote: Dear all, My apologies for the spam-like nature of my post, but I would like to draw your attention to an important issue (outlined in an upcoming short communication to Acta D, which will appear at doi:10.1107/S1399004715000826 once it's online). At present, neither the structural quality checks in commonly-used crystallography packages nor those run on deposition of a structure to the PDB are flagging the presence of non-proline cis peptide bonds. This has led to the presence of many erroneous cis bonds creeping into the PDB - primarily in low-resolution structures as one would expect, but I have identified clearly erroneous examples in structures with resolutions as high as 1.3 Angstroms. From my analysis, I estimate that a few thousand structures have been affected to some extent, with the worst cases having as high as 3% of their peptide bonds in cis. Particularly if you have published anything >2.5 Angstroms in the past few years, may I gently suggest that you make a quick double-check of your deposited structures? This can be done quickly and simply in Coot (Extensions-Modelling-Residues with Cis peptide bonds). Best regards, Tristan Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.
