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?
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-----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.
