Trevor, I can share our recent experience correcting the record about a misplaced ligand binding site. It represents one possible way to deal with erroneous structures.
Our analysis of structures of the proline biosynthetic enzyme PYCR1 deposited by another group in 2006 suggested that the NAD(P)H cofactor had been erroneously modeled into noise density, placing the ligand over 25 Angstrom from the canonical binding site for Rossmann fold enzymes. Because of our longstanding interest in proline metabolism, I felt compelled to set the record straight. Therefore, we generated a clone, purified the protein, and determined several structures with different ligands bound. Sure enough, the ligands in the 2006 structures were incorrect. The supplement to our paper includes a thorough analysis of the electron density of the incorrect structures (EDS maps, PDBREDO, and omit maps). We also did kinetics and analytical ultracentrifugation studies. In short, we did a fairly comprehensive biochemical and biophysical study of the enzyme. Thus, pointing out someone else’s error was just one part of a larger paper. http://faculty.missouri.edu/%7Etannerjj/tannergroup/pdfs/PYCR1JBC2017withSupp.pdf<http://faculty.missouri.edu/~tannerjj/tannergroup/pdfs/PYCR1JBC2017withSupp.pdf> https://www.ncbi.nlm.nih.gov/pubmed/28258219 Jack Tanner John J. Tanner Professor of Biochemistry and Chemistry Chair, Biochemistry Department Graduate Admissions Committee Department of Biochemistry University of Missouri-Columbia 117 Schweitzer Hall Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-5635 Email: tanne...@missouri.edu<mailto:tanne...@missouri.edu> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A On Jun 27, 2017, at 1:34 AM, Trevor Sewell <trevor.sew...@uct.ac.za<mailto:trevor.sew...@uct.ac.za>> wrote: 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<mailto:cs...@uct.ac.za>
