This reminds me of:
Pig heart short chain L-3-hydroxyacyl-CoA dehydrogenase revisited:
Sequence analysis and crystal structure determination
Barycki JJ, O'Brien LK, Birktoft JJ, Strauss AW, Banaszak LJ
Protein Science (Oct 1999) Vol 8, pp 2010-2018.
In which the protein in question also had one monomer forming a dimer
about a crystallographic axis, and two monomers forming a dimer
elsewhere in the asymmetric unit.
A portion of the molecule had messy density, which caused difficulties
literally for decades. The eventual solution was to switch to a
different species (human). After which, a MR solution of the original
porcine data was possible. I believe the disorder was judged to be
intrinsic.
On 05/19/11 09:02, Joane Kathelen Rustiguel wrote:
Dear all
I am refining a structure at 3.4 A resolution that contains 3 molecules in the
a.u. The chain A sits on a 2-fold crystallographic axis forming the dimeric
functional structure expected for this class of proteins. The other two chains
B and C, which also form the functional dimer, seem to be, somehow, a lot more
flexible than chain A. As a result, whereas the electron density map, b-factor
and geometry for chain A is pretty reasonable for a 3.4 A resolution
structure, the refinement for the other two chains (B and C) does not behave
well. Even playing with different weights for geometry, analysing different
levels of 2Fo-Fc/Fo-Fc maps, using NCS, TLS, etc..., nothing works. The map
for the helical regions is ok, but the electron density map for strands and
loops of chains B and C are broken along the main chain, B-factors are really
high, and the geometry keeps being distorted.
Right now, the R-factor and R-free are 24.2 and 28.6, respectively.
Any suggestions in how to proceed the refinement?
And even a more difficult question, how do we report this type of structure?
How do we deposit those coordinates? We can certainly use chain A as a model
to perform interesting studies of structure-function relationship, but we know
that chain B and chain C have problems.
Any help will be greatly appreciated.
Regards
Joane
--
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All Things Serve the Beam
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David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
