2q3u: Difference between revisions

Revision as of 12:37, 10 July 2008

This article has been automatically seeded. Changes to this page should pertain to the PDB entry only and not to the protein or biomolecule in general.

File:2q3u.png

Template:STRUCTURE 2q3u

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolaseEnsemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolase

Template:ABSTRACT PUBMED 17850744

About this StructureAbout this Structure

2Q3U is a Single protein structure of sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA.

ReferenceReference

Ensemble refinement of protein crystal structures: validation and application., Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr, Structure. 2007 Sep;15(9):1040-52. PMID:17850744

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-'''Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolase'''
+===Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolase===
-==Overview==
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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.
+The line below this paragraph, {{ABSTRACT_PUBMED_17850744}}, adds the Publication Abstract to the page
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 [[Category: Refinement methodology development]]
 [[Category: Structural genomic]]
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