2q4d: Difference between revisions

Revision as of 14:07, 23 January 2008

Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At5g11950

OverviewOverview

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.

About this StructureAbout this Structure

2Q4D is a Single protein structure of sequence from Arabidopsis thaliana with and as ligands. 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

Page seeded by OCA on Wed Jan 23 13:07:38 2008

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OCA

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-[[Image:2q4d.jpg|left|200px]]<br /><applet load="2q4d" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:2q4d.jpg|left|200px]]<br /><applet load="2q4d" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="2q4d, resolution 2.152&Aring;" />
 '''Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At5g11950'''<br />
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 ==About this Structure==
-Q4D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] with NO3 and EDO as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2Q4D OCA].
+Q4D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] with <scene name='pdbligand=NO3:'>NO3</scene> and <scene name='pdbligand=EDO:'>EDO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4D OCA].
 ==Reference==
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 [[Category: unknown function]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 13:47:58 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 13:07:38 2008''