2q43: Difference between revisions

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Revision as of 07:41, 26 March 2008

File:2q43.jpg

, resolution 2.000Å

Gene:

ILL2, At5g56660, MIK19.11 (Arabidopsis thaliana)

Domains:

PRK13009, AbgB, M20_dimer

Resources:

FirstGlance, OCA, PDBsum, JenaLib, RCSB

Coordinates:

save as pdb, mmCIF, xml

Ensemble refinement of the protein crystal structure of IAA-aminoacid hydrolase from Arabidopsis thaliana gene At5g56660

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

2Q43 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 Wed Mar 26 06:41:21 2008

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

OCA

@@ Line 7: / Line 7: @@
 |ACTIVITY=
 |GENE= ILL2, At5g56660, MIK19.11 ([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=PRK13009 PRK13009], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG1473 AbgB], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam07687 M20_dimer]</span>
+|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q43 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q43 OCA], [http://www.ebi.ac.uk/pdbsum/2q43 PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=2q43 RCSB]</span>
 }}
@@ Line 40: / Line 42: @@
 [[Category: structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:21:22 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 06:41:21 2008''