Hi Trevor, Some of my colleagues came across a misinterpreted structure published in Acta D., a couple of years ago. They raised the issue with the editors of Acta D., who were most helpful in getting the issue sorted out.
My impression is that the journals are the responsible for the papers that they publish, and raising this type of issue with the journal editors initially - may be the best way forward. Best regards, Ben On 27 Jun 2017, at 08:15, Trevor Sewell <trevor.sew...@uct.ac.za> wrote: The misinterpretation is considerable I as can be seen from the attached coot screenshot. I have no reason to suspect malfeasance. But it looks like the authors didn’t check very carefully. I have re-interpreted and refined the density and it is just fine – Rfactor of 18% for a 2.3A structure. The critical reinterpretations concern the orientation of the backbone near the active site and the interpretation of a blob of density claimed to be substrate in the original paper. Maybe the best would be to write to the author and suggest that she obsolete the structure. We could see if we could reach some agreement on how to take it further – perhaps a letter to the editor of JBC. Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 From: Manfred S. Weiss <mailto:manfred.we...@helmholtz-berlin.de> Sent: Tuesday, June 27, 2017 8:46 AM To: Trevor Sewell <mailto:trevor.sew...@uct.ac.za> Subject: Re: [ccp4bb] Incorrect Structure in the PDB Dear Trevor, you can download the incorrect structure and the associated data and reinterpret and re-refine the structure. Then you can re-deposit provided you write a paper about the new findings. This is currently the policy of the PDB. Else, you can contact the authors of the incorrect structure and do the reinterpretation together with them? They can replace the incorrect structure without a new publication. That's all there is at the moment. May I ask what is incorrect about the structure? Cheers, Manfred Am 27.06.2017 um 08:34 schrieb Trevor Sewell: > > I have come across a key paper in my field that describes an enzyme > mechanism. Their work is based on a deposited structure – by other authors - > that is incorrectly interpreted. > > Is there a process for removing a demonstrably wrong structure (deposited by > others) from the PDB and replacing it with a correctly interpreted structure > based on the original data? Or is there an alternative, and generally > recognized, way of getting the correct structure in the public domain? > > Many thanks for your advice on this matter. > > Trevor Sewell > > Disclaimer - University of Cape Town This e-mail is subject to UCT policies > and e-mail disclaimer published on our website > athttp://www.uct.ac.za/about/policies/emaildisclaimer/ > <https://protect-za.mimecast.com/s/vQqAB6SaJ5drIw> or obtainable from +27 21 > 650 9111. If this e-mail is not related to the business of UCT, it is sent by > the sender in an individual capacity. Please report security incidents or > abuse via cs...@uct.ac.za <mailto:cs...@uct.ac.za> -- Dr. Manfred S. Weiss Macromolecular Crystallography Helmholtz-Zentrum Berlin Albert-Einstein-Str. 15 D-12489 Berlin Germany Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. Jutta Koch-Unterseher Geschäftsführung: Prof. Dr. Bernd Rech (kommissarisch), Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de <https://protect-za.mimecast.com/s/ndaRBlf2pwDnU4> Disclaimer - University of Cape Town This e-mail is subject to UCT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ <http://www.uct.ac.za/about/policies/emaildisclaimer/> or obtainable from +27 21 650 9111. If this e-mail is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via cs...@uct.ac.za <mailto:cs...@uct.ac.za><Around residue 228.png> Dr Ben Bax York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD ben.d.v....@gmail.com
