2q4n: Difference between revisions

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Revision as of 04:44, 31 March 2008

File:2q4n.jpg

, resolution 1.320Å

Ligands:

Gene:

At1g79260, YUP8H12R.14 (Arabidopsis thaliana)

Domains:

DUF1794

Related:

2A13

Resources:

FirstGlance, OCA, PDBsum, RCSB

Coordinates:

save as pdb, mmCIF, xml

Ensemble refinement of the crystal structure of protein from Arabidopsis thaliana At1g79260

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

2Q4N 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 Mon Mar 31 04:44:39 2008

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

OCA

@@ Line 8: / Line 8: @@
 |GENE= At1g79260, YUP8H12R.14 ([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=pfam08768 DUF1794]</span>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4n OCA], [http://www.ebi.ac.uk/pdbsum/2q4n PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=2q4n RCSB]</span>
+|RELATEDENTRY=[[2a13|2A13]]
+|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4n OCA], [http://www.ebi.ac.uk/pdbsum/2q4n PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2q4n RCSB]</span>
 }}
@@ Line 39: / Line 40: @@
 [[Category: unknown function]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 06:41:54 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:44:39 2008''