2q4j: Difference between revisions

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[[Image:2q4j.jpg|left|200px]]
{{Seed}}
[[Image:2q4j.png|left|200px]]


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{{STRUCTURE_2q4j|  PDB=2q4j  |  SCENE=  }}  
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'''Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g03250, a putative UDP-glucose pyrophosphorylase'''
===Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g03250, a putative UDP-glucose pyrophosphorylase===




==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.
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{{ABSTRACT_PUBMED_17850744}}


==About this Structure==
==About this Structure==
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[[Category: Structural genomic]]
[[Category: Structural genomic]]
[[Category: Transferase]]
[[Category: Transferase]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 14:19:51 2008''
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 10 12:37:08 2008''

Revision as of 09:37, 10 July 2008

File:2q4j.png

Template:STRUCTURE 2q4j

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g03250, a putative UDP-glucose pyrophosphorylase

Template:ABSTRACT PUBMED 17850744

About this Structure

2Q4J is a Single protein structure of sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA.

Reference

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

Page seeded by OCA on Thu Jul 10 12:37:08 2008

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