It can't hurt to try to work with the author, and it's the only way to get the current PDB file out of the database. If you don't get the response you want you can still go ahead and look for a venue to publish your own interpretation.
Having a paper to go with the model is not only a requirement of the wwPDB rules but it makes the situation much clearer the someone wanting to understand this protein. Having a second model in the PDB w/o a publication would not leave many clues to decide which model to use. Dale Tronrud On 6/27/2017 12:15 AM, Trevor Sewell 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 at >> 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 > > -- > 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/ 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
