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PDBsum entry 2q4d
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Structural genomics, unknown function
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PDB id
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2q4d
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References listed in PDB file
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Key reference
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Title
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Ensemble refinement of protein crystal structures: validation and application.
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Authors
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E.J.Levin,
D.A.Kondrashov,
G.E.Wesenberg,
G.N.Phillips.
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Ref.
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Structure, 2007,
15,
1040-1052.
[DOI no: ]
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PubMed id
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Abstract
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X-ray crystallography typically uses a single set of coordinates and B factors
to describe macromolecular conformations. Refinement of multiple copies of the
entire structure has been previously used in specific cases as an alternative
means of representing structural flexibility. Here, we systematically validate
this method by using simulated diffraction data, and we find that ensemble
refinement produces better representations of the distributions of atomic
positions in the simulated structures than single-conformer refinements.
Comparison of principal components calculated from the refined ensembles and
simulations shows that concerted motions are captured locally, but that
correlations dissipate over long distances. Ensemble refinement is also used on
50 experimental structures of varying resolution and leads to decreases in
R(free) values, implying that improvements in the representation of flexibility
observed for the simulated structures may apply to real structures. These gains
are essentially independent of resolution or data-to-parameter ratio, suggesting
that even structures at moderate resolution can benefit from ensemble refinement.
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Figure 2.
Figure 2. Examples of Anharmonic Residue Probability
Distributions for the Simulated Single- and Multiple-Conformer
Models
The panels on the left show images of the electron
density maps generated from the MD simulations of 1Q4R, along
with a stick representation of the final 16-conformer model. The
panels on the right show, for the red residues, the histograms
of the projections of the simulation coordinates along the first
principal components (shown in black), as well as the
probability density functions calculated from the 1-conformer
(red) and 16-conformer (blue) models along the same axis.
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Figure 6.
Figure 6. Effect of Observation-to-Parameter Ratio on the
Improvement in R[free] from Ensemble Refinement
The
decrease in the R[free] value between the initial R[free] value
and the R[free] value of the best-performing multiple-conformer
model for the 50 experimental structures is plotted as a
function of the ratio of the number of reflections used in the
refinement to the number of atoms in the original one-conformer
structure.
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The above figures are
reprinted
from an Open Access publication published by Cell Press:
Structure
(2007,
15,
1040-1052)
copyright 2007.
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Secondary reference #1
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Title
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X-Ray crystal structures of the conserved hypothetical proteins from arabidopsis thaliana gene loci at5g11950 and at2g37210.
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Authors
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W.B.Jeon,
S.T.Allard,
C.A.Bingman,
E.Bitto,
B.W.Han,
G.E.Wesenberg,
G.N.Phillips.
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Ref.
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Proteins, 2006,
65,
1051-1054.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. (A) Ribbon diagram of the At5g11950 dimer with each
monomer colored separately. (B) An overlay of C  traces
of At5g11950 (red) and At2g37210 (cyan). The residues
corresponding to helix 3
and neighboring loops adopt a defined structure within At5g11950
(red). The same region is disordered in the At2g37210 structure
(cyan). A fully conserved residue, Arg98, and the PGGxGTxxE
motif, which is highly conserved among the LDC like
proteins,[15] were mapped onto a C trace
of the At5g11950 structure. (C) Surface view of the two monomers
(yellow and cyan) in the At2g37210 dimer. The dark blue area
represents the conserved motif PGGxGTxxE and residue Arg98,
located at the bottom of a cavity. The red line highlights the
residues corresponding to helix 3
of At5g11950. These residues are positioned near the entrance to
the cavity and are disordered in the crystal structure of
At2g37210, suggesting that they may be involved in controlling
access of a substrate to the putative active site.
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The above figure is
reproduced from the cited reference
with permission from John Wiley & Sons, Inc.
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