2q4m

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|PDB= 2q4m |SIZE=350|CAPTION= <scene name='initialview01'>2q4m</scene>, resolution 1.700&Aring;
|PDB= 2q4m |SIZE=350|CAPTION= <scene name='initialview01'>2q4m</scene>, resolution 1.700&Aring;
|SITE=
|SITE=
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|LIGAND= <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>
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|LIGAND= <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>
|ACTIVITY=
|ACTIVITY=
|GENE= At5g01750, T20L15.20 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])
|GENE= At5g01750, T20L15.20 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])
 +
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam04525 DUF567]</span>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4m OCA], [http://www.ebi.ac.uk/pdbsum/2q4m PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=2q4m RCSB]</span>
}}
}}
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[[Category: Levin, E J.]]
[[Category: Levin, E J.]]
[[Category: Wesenberg, G E.]]
[[Category: Wesenberg, G E.]]
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[[Category: EDO]]
 
[[Category: at5g01750]]
[[Category: at5g01750]]
[[Category: center for eukaryotic structural genomic]]
[[Category: center for eukaryotic structural genomic]]
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[[Category: unknown function]]
[[Category: unknown function]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:21:37 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 06:41:52 2008''

Revision as of 04:41, 26 March 2008

Image:2q4m.jpg


PDB ID 2q4m

Drag the structure with the mouse to rotate
, resolution 1.700Å
Ligands: ,
Gene: At5g01750, T20L15.20 (Arabidopsis thaliana)
Domains: DUF567
Resources: FirstGlance, OCA, PDBsum, JenaLib, RCSB
Coordinates: save as pdb, mmCIF, xml



Ensemble refinement of the crystal structure of protein from Arabidopsis thaliana At5g01750


Overview

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 Structure

2Q4M 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

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