2q4w

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 8: Line 8:
|GENE= CKX7, CKX5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])
|GENE= CKX7, CKX5 ([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=pfam09265 Cytokin-bind], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam01565 FAD_binding_4]</span>
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam09265 Cytokin-bind], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam01565 FAD_binding_4]</span>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4w OCA], [http://www.ebi.ac.uk/pdbsum/2q4w PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=2q4w RCSB]</span>
+
|RELATEDENTRY=[[2exr|2EXR]]
 +
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q4w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4w OCA], [http://www.ebi.ac.uk/pdbsum/2q4w PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2q4w RCSB]</span>
}}
}}
Line 42: Line 43:
[[Category: structural genomic]]
[[Category: structural genomic]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 06:42:09 2008''
+
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:44:48 2008''

Revision as of 01:44, 31 March 2008

Image:2q4w.jpg


PDB ID 2q4w

Drag the structure with the mouse to rotate
, resolution 1.700Å
Sites:
Ligands: ,
Gene: CKX7, CKX5 (Arabidopsis thaliana)
Activity: Cytokinin dehydrogenase, with EC number 1.5.99.12
Domains: Cytokin-bind, FAD_binding_4
Related: 2EXR


Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



Ensemble refinement of the protein crystal structure of cytokinin oxidase/dehydrogenase (CKX) from Arabidopsis thaliana At5g21482


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

2Q4W 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

Page seeded by OCA on Mon Mar 31 04:44:48 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2q4w"
Personal tools