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.
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