[buster-discuss] Refine occupancy on two different polypeptide chains
Anna Suarez Larsson
anna at xray.bmc.uu.se
Fri Jan 26 10:17:01 CET 2018
Dear Buster users,
I am dealing with a pentameric structure composed of two different short (80 aa) polypeptide chains, A and B, that are 40% identical. In the crystal packing it looks to be no preferred orientation for the ring with respect to the two different proteins. I would like to combine the two chains in the same structure and refine with Buster to get the relative occupancy. We know from gel electrophoresis of the two proteins coexpressed that the relation is 3:2 (A to B) between them, both in crystals and in solution. The crystals diffract to about 2.0 Å resolution but the spots are streaky. The R-values when refining with only one of the polypeptide chains are much lower for A compared to B.
My attempt to do the refinement in Buster using first pdb2occ and then run with the command -Gelly failed with the comment:
Interpreting CONSTANT and FREE cards:
=====NOTE BUSTER_CONSTANT OCC FixOcc
*** ERROR found in interpreting atom specifier from CONSTANT card
*** ERROR specifier=FixOcc
*** ERROR does not match any atoms
*** ERROR *** found processing constant cards
*** ERROR *** (on call to GELLY_PROCESS_CONSTANT_CARDS_OWN
*** ERROR *** by s/r GELLY_PROCESS_CONST_COMBINE_CARDS_OWN)
How should I do to be able to proceed? Is it possible to refine double occupancy on all the five polypeptide chains or is it required that I keep some of them with fixed occupancy?
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