2q4e: Difference between revisions

Revision as of 14:19, 4 May 2008

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At4g09670

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

2Q4E 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 Page seeded by OCA on Sun May 4 14:19:18 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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 [[Image:2q4e.jpg|left|200px]]
- {{Structure
+<!--
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+The line below this paragraph, containing "STRUCTURE_2q4e", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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+or leave the SCENE parameter empty for the default display.
-|GENE= At4g09670, F17A8.20 ([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=pfam01408 GFO_IDH_MocA], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG0673 MviM]</span>
+{{STRUCTURE_2q4e|  PDB=2q4e  |  SCENE=  }}
-|RELATEDENTRY=[[1ydw|1YDW]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4e OCA], [http://www.ebi.ac.uk/pdbsum/2q4e PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2q4e RCSB]</span>
-}}
 '''Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At4g09670'''
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 [[Category: Levin, E J.]]
 [[Category: Wesenberg, G E.]]
-[[Category: at4g09670]]
+[[Category: At4g09670]]
-[[Category: center for eukaryotic structural genomic]]
+[[Category: Center for eukaryotic structural genomic]]
-[[Category: cesg]]
+[[Category: Cesg]]
-[[Category: ensemble refinement]]
+[[Category: Ensemble refinement]]
-[[Category: oxidoreductase]]
+[[Category: Oxidoreductase]]
-[[Category: protein structure initiative]]
+[[Category: Protein structure initiative]]
-[[Category: psi]]
+[[Category: Psi]]
-[[Category: refinement methodology development]]
+[[Category: Refinement methodology development]]
-[[Category: structural genomic]]
+[[Category: Structural genomic]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 14:19:18 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:44:29 2008''