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PDBsum entry 2q4t
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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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Structure of pyrimidine 5'-Nucleotidase type 1. Insight into mechanism of action and inhibition during lead poisoning.
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Authors
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E.Bitto,
C.A.Bingman,
G.E.Wesenberg,
J.G.Mccoy,
G.N.Phillips.
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Ref.
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J Biol Chem, 2006,
281,
20521-20529.
[DOI no: ]
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PubMed id
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Figure 2.
FIGURE 2. Comparison of mP5N-1 and its closest structural
homolog. A, a stereo representation of structural superposition
of mP5N-1 (red; Protein Data Bank code 2bdu) and hPSP (cyan;
Protein Data Bank code 1l8o). Every 10th C[  ]carbon of mP5N-1 is
highlighted by a red sphere, and some are labeled by residue
numbers for better orientation. B, structural superposition of
the active sites of mP5N-1 (red) and hPSP (cyan; Protein Data
Bank code 1nnl).
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Figure 3.
FIGURE 3. The reaction scheme of mP5N-1. A, mP5N-1 has two
enzymatic activities: nucleotidase activity (steps 1 and 2a) and
phosphotransferase activity (steps 1 and 2b). B, the proposed
catalytic mechanism for nucleotidase activity of mP5N-1. "R"
represents ribonucleoside. Individual states of the reaction
mechanism include apoenzyme (I), active enzyme (II), the
substrate complex (III), the substrate-transition complex (IV),
the phosphoenzyme intermediate (V), the product-transition
complex (VI), and the product complex (VII).
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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