2q4w

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
[[Image:2q4w.jpg|left|200px]]<br /><applet load="2q4w" size="350" color="white" frame="true" align="right" spinBox="true"
+
[[Image:2q4w.jpg|left|200px]]
-
caption="2q4w, resolution 1.700&Aring;" />
+
 
-
'''Ensemble refinement of the protein crystal structure of cytokinin oxidase/dehydrogenase (CKX) from Arabidopsis thaliana At5g21482'''<br />
+
{{Structure
 +
|PDB= 2q4w |SIZE=350|CAPTION= <scene name='initialview01'>2q4w</scene>, resolution 1.700&Aring;
 +
|SITE= <scene name='pdbsite=AC1:Fad+Binding+Site+For+Residue+A+701'>AC1</scene>
 +
|LIGAND= <scene name='pdbligand=FAD:FLAVIN-ADENINE DINUCLEOTIDE'>FAD</scene>
 +
|ACTIVITY= [http://en.wikipedia.org/wiki/Cytokinin_dehydrogenase Cytokinin dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.99.12 1.5.99.12]
 +
|GENE= CKX7, CKX5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])
 +
}}
 +
 
 +
'''Ensemble refinement of the protein crystal structure of cytokinin oxidase/dehydrogenase (CKX) from Arabidopsis thaliana At5g21482'''
 +
 
==Overview==
==Overview==
Line 7: Line 16:
==About this Structure==
==About this Structure==
-
2Q4W is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] with <scene name='pdbligand=FAD:'>FAD</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Cytokinin_dehydrogenase Cytokinin dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.99.12 1.5.99.12] Known structural/functional Site: <scene name='pdbsite=AC1:Fad+Binding+Site+For+Residue+A+701'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4W OCA].
+
2Q4W is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4W OCA].
==Reference==
==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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17850744 17850744]
+
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:[http://www.ncbi.nlm.nih.gov/pubmed/17850744 17850744]
[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
[[Category: Cytokinin dehydrogenase]]
[[Category: Cytokinin dehydrogenase]]
Line 32: Line 41:
[[Category: structural genomic]]
[[Category: structural genomic]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Mar 14 09:43:09 2008''
+
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:21:44 2008''

Revision as of 16:21, 20 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
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 Thu Mar 20 18:21:44 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

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