Hi Andrew, One of the atoms should be in altconf A and the other in B. Otherwise the problem remains.
Pedro Às 01:48 de 20/12/2016, Andrew Marshall escreveu: > Hi all, > > Thank you for your suggestions. I tried the pdb file edit (making the > offending atoms of both the ligand and the protein 'B' altconf), but > it didn't seem to make any difference to their positions after a > single round of refinement..? > The atoms in the active site concern two acetyl groups - one from the > substrate, acetyl-CoA, and the other from an acetylated cysteine in > the protein - that I believe are poised ready for a condensation > reaction. The closest contacts are between S and O(carbonyl) atoms > (2.9A) and O and CH3 (3.1A), but going off the density, I think these > should be closer (more like 2.8 or 2.7A). It may be that I've trapped > another reaction intermediate (which would be cool), but I don't think > that fits the density quite as well. Any thoughts/ideas? > > Thanks, > > Andrew Marshall > PhD Candidate > Laboratory of Protein Crystallography > Dept. of Molecular and Cellular Biology > School of Biological Sciences > The University of Adelaide > > On Tue, Dec 20, 2016 at 12:09 AM, Scott Horowitz <horow...@umich.edu > <mailto:horow...@umich.edu>> wrote: > > Hi Andrew, > > I'm curious- what are the atoms that are clashing? I worked on > this sort of thing back in my Ph.D., and so I might have some > useful tidbits if, for example, the S is clashing with a carbon of > some sort. > > Thanks, > Scott > > On Mon, Dec 19, 2016 at 12:39 AM, Andrew Marshall > <andrew.c.marsh...@adelaide.edu.au > <mailto:andrew.c.marsh...@adelaide.edu.au>> wrote: > > Hi all, > > I have a structure of a condensing enzyme with substrate > bound. The active site is very tight, requiring some of the > substrate atoms to clash with a catalytic cysteine. This means > that although the substrate fits the density nicely upon > manual real-space refinement, phenix recognises the clash, > resulting in the displacement of substrate atoms so that they > are outside the density. I can mostly fix this by using > distance restraints, but I'd rather allow it to refine in a > less biased manner, but ignore the clash. Is this a acceptable > way forward? If so, is there a parameter I can edit to tell > phenix to ignore clashes between these specific atoms? > > Thanks, > > Andrew Marshall > PhD Candidate > Laboratory of Protein Crystallography > Dept. of Molecular and Cellular Biology > School of Biological Sciences > The University of Adelaide > > > > > -- > Scott Horowitz, Ph.D. > Postdoctoral Fellow > > University of Michigan > Department of Molecular, Cellular, and Developmental Biology > Bardwell lab > 830 N. University Ave, Room 4007 > Ann Arbor, MI 48109 > phone: 734-647-6683 > fax: 734-615-4226 > > -- Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___________________________________ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21) 441-1277 or 443-3644 email : mat...@itqb.unl.pt http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit Mailing address : Instituto de Tecnologia Quimica e Biologica António Xavier Universidade Nova de Lisboa Av. da República 2780-157 Oeiras PORTUGAL ITQB NOVA, a great choice for your PhD https://youtu.be/de6j-aaTWNQ Master Programme in Biochemistry for Health https://youtu.be/UKstDCFjYI8
