Re: [ccp4bb] geometry problems with sugars

[tirumal]

Thanks to all who responded. 180 degrees flip of the problematic NAGs, did help.

 At the moment, there is no substitute for knowledge when building 
carbohydrates - it would be a substantial improvement I think if someone
 added intelligent carbohydrate validation tools into Coot.

If you have a poor density (which I guess, generally is the case for large 
glycoprotein structures) you have to depend on trial and error strategy to get 
the right NAG conformation. I don't know how other refinement programs handle 
this, but after Phenix.refinement run, one has to definitely check the geometry 
of the NAGs carefully.

Hope to see a validation tool for NAGs in Coot soon.

Tirumal

 




--- On Wed, 21/4/10, Garib Murshudov ga...@ysbl.york.ac.uk wrote:

From: Garib Murshudov ga...@ysbl.york.ac.uk
Subject: Re: [ccp4bb] geometry problems with sugars
To: CCP4BB@JISCMAIL.AC.UK
Date: Wednesday, 21 April, 2010, 9:58

JED's example is very illustrative and it shows that chirality may need to be 
added to this link definition. then sugar validation may be easier (at least 
ASN-NAG with only one sugar). If chirality is wrong then rotate around 
ND2-C1bond as a rigid group. Just like you do with rotamers. Here you have only 
two orientations.

Garib

On 21 Apr 2010, at 14:20, Paul Emsley wrote:

 Garib Murshudov wrote:
 As I see there is no chirality definition for NAG-ASN link (perhaps  there 
 should be but then people will be unhappy even more).
 Only reason i can see for this flattening is conflict between geometry  and 
 electron density. Your example shows that even if electron density  is weak 
 it may play a role and correct orientation of sugar may matter.
 
 
 I agree, and with JED too.  More tests suggest that if I put the NAG into the 
 density the wrong way round, Coot will happily flatten the C1.  So, my guess 
 would be that if you rotated your NAG 180 degrees round a vector ~ 
 NG--(midpoint of C3,C4) and re-refined, then things would improve.
 
 At the moment, there is no substitute for knowledge when building 
 carbohydrates - it would be a substantial improvement I think if someone 
 added intelligent carbohydrate validation tools into Coot.
 
 Paul.



  

[ccp4bb] geometry problems with sugars

[tirumal]

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