[ccp4bb] geometry problems with sugars

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: Proportion of MR in PDB
From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2010-04-20

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From: Patrick Loll pat {- dot -} loll {- at -} DREXEL {- dot -} EDU
Date: 2010-04-20

Subject: geometry problems with sugars
From: tirumal ch_tirumal {- at -} YAHOO {- dot -} COM
Date: 2010-04-20

Hi All,

My question is concerning geometry of NAGs in a glycoprotein structure.

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.

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). 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.

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.

Then, I tried replacing the NAGs with ideal monomers from Coot. Still, the problem persisted. PDB annotator's suggestion is to get the NAG coordinates from HIC-Up and try refinement in another program.

I am wondering if any one else noticed (or had ) a similar problem with NAG geometry using either Phenix.refine or Coot. What baffles me is that the ideal NAG from coot dictionary did not pass the internal validation of the PDB.

I would appreciate if any one has any suggestion (other than trying a different refinement program) to get around this problem. Is there a way to compare the NAGs in your structure to the ideal and get to know what to fix ?

Thanks in advance

Tirumal

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Proportion of MR in PDB
From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2010-04-20

Next message:
Subject: Re: chiral volumes--2nd try
From: Patrick Loll pat {- dot -} loll {- at -} DREXEL {- dot -} EDU
Date: 2010-04-20