I've seen flattening of the C1 atom recently in Coot - in that case the reason was that, as the density wasn't really clear around the sugar, I'd fitted it 180 degrees rotated around the ASN-ND2---C1-NAG bond. In such cases Coot happily flattens the sugar ring such that C1 C2 C3 C5 O5 are in a plane, just locked half way between chair and boat.
Bug? Or yet another bite of the torsions/chiralities monster? -------------------------------------------------------------------------- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 15 Stanhope Gate, London W1K 1LN. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -----Original Message----- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Paul Emsley Sent: 20 April 2010 23:57 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] geometry problems with sugars tirumal wrote: > Hi All, > > My question is concerning geometry of NAGs in a glycoprotein structure. > Fire away... > > I recently solved the structure of a glycoprotein to 3 Å and modeled > NAGs linked to Asn at 3 different places. NAGs and Asn-NAG links are > refined in Phenix.refine as per the Phenix dictionary. > Errr.. that'll be the Refmac dictionary. > > However, when submitting the structure to the PDB, internal validation > of PDB found that NAGs at 2 places have geometry problems (atoms > surrounding the C1 of NAG are in the same plane). > The surrounding atoms being the ND2, O5 and C2, I presume. The C1 should not (of course) be in the plane of those 3 atoms. > What I learned from Phenix bulletin board is that the refinement > program is probably fixing the NAG into a local minimal structure to > fit to the density the best (I have OK density for sugars) and that's > causing the problem. > It seems unlikely to me that you density would be sufficiently strong to put C1, ND2, O5 and C2 into a plane. > > So, I tried to fix the geometry of NAG while refining, so that the > refinement does not change the geometry of the sugar. But, still the > internal validation of PDB found the same problem with the sugars. > I don't follow this. How can you fix the atoms of the NAG and then refine it (and expect things to move)? > > Then, I tried replacing the NAGs with ideal monomers from Coot. > "Get Monomer" in Coot use LIBCHECK to generate coordinates and restraints. I can use "Get Monomer" to import a NAG and create and refine a N-link quite happily (after deleting the O1 and HO1 of course - Coot won't do that for you yet). > Still, the problem persisted. PDB annotator's suggestion is to get the > NAG coordinates from HIC-Up and try refinement in another program. > A very worthy path to pursue... > > I am wondering if any one else noticed (or had ) a similar problem > with NAG geometry using either Phenix.refine or Coot. > I don't see a problem. > What baffles me is that the ideal NAG from coot dictionary did not > pass the internal validation of the PDB. > I'd find that surprising too (and to be accurate, it's from LIBCHECK and just imported into Coot). > > I would appreciate if any one has any suggestion (other than trying a > different refinement program) to get around this problem. > Perish the thought of suggesting a CCP4 refinement program on this list... :) > Is there a way to compare the NAGs in your structure to the ideal and > get to know what to fix ? > > I must admit that I'm curious to know what the PDB has against CCP4's NAG. HTH, Paul.
