Hello,
I'm having problems adding XYP (beta-xylose) to my glycosylation chain in a
plant protein.
I have a 1.87 Angstrom map, 4 molecules in the asymmetric unit. I have two
primary N-glycosylation sites, per protein. I am not using NCS for refinement
or model building.
The density for the NAG-(FUC)-NAG is very clear at both sites of all molecules
in the a.u. The BMA (beta mannose after the 2nd NAG) is clear at one of the
glycosylation sites. At this glycosylation site, I see good density for a MAN
at the C3 and C6 sites of BMA. I can see good density for a xylose at the C2 -
it is really quite clear.
Using COOT, and the Glyco module, set to Hybrid (Plant), I have been able to
add all the NAGs, MANs, and FUCs with a press of a mouse button. It is a *very
nice* function of COOT.
But..... I can't get the XYP added correctly. I select the "add an XYP-BMA
XYP", and it pops the XYP where I want it, but then it rapidly wiggles away.
It is as if it is actively finding an area of no density (I am not
exaggerating). Selecting 'Refine Tree' does not resolve the problem. I've
tried manually moving the xylose close enough, but this is not working well.
It just refines away in Phenix Refine.
For refinement, I used ReadySet to generate the restraints (apparently the
XYP-BMA XYP does not have restraints in the standard library - is that correct?)
This is a big enough problem, I am hoping I am just doing something 'big' that
is wrong. I'm assuming (perhaps) it is a library problem. I would appreciate
any suggestions.
Software details:
On Windows, WinCoot 0.8.9
On Mac, Phenix version 1.13-29998-000 (Coot is version 0.8.9)
I model build in WinCoot, refine with Phenix on the Mac
Regards,
Marilyn
___________________________________________________________
Marilyn Yoder | 816-235-1986 | SCB 526 | Division of Cell Biology &
Biophysics, University of Missouri-Kansas City
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