2q4w
From Proteopedia
| Line 2: | Line 2: | ||
caption="2q4w, resolution 1.700Å" /> | caption="2q4w, resolution 1.700Å" /> | ||
'''Ensemble refinement of the protein crystal structure of cytokinin oxidase/dehydrogenase (CKX) from Arabidopsis thaliana At5g21482'''<br /> | '''Ensemble refinement of the protein crystal structure of cytokinin oxidase/dehydrogenase (CKX) from Arabidopsis thaliana At5g21482'''<br /> | ||
| + | |||
| + | ==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== | ==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 [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]. | ||
| + | |||
| + | ==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] | ||
[[Category: Arabidopsis thaliana]] | [[Category: Arabidopsis thaliana]] | ||
[[Category: Cytokinin dehydrogenase]] | [[Category: Cytokinin dehydrogenase]] | ||
| Line 15: | Line 21: | ||
[[Category: FAD]] | [[Category: FAD]] | ||
[[Category: at5g21482 1]] | [[Category: at5g21482 1]] | ||
| - | [[Category: center for eukaryotic structural | + | [[Category: center for eukaryotic structural genomic]] |
[[Category: cesg]] | [[Category: cesg]] | ||
[[Category: ckx]] | [[Category: ckx]] | ||
| Line 24: | Line 30: | ||
[[Category: psi]] | [[Category: psi]] | ||
[[Category: refinement methodology development]] | [[Category: refinement methodology development]] | ||
| - | [[Category: structural | + | [[Category: structural genomic]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Mar 14 09:43:09 2008'' |
Revision as of 07:43, 14 March 2008
|
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 with as ligand. Active as Cytokinin dehydrogenase, with EC number 1.5.99.12 Known structural/functional Site: . 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 Fri Mar 14 09:43:09 2008
Categories: Arabidopsis thaliana | Cytokinin dehydrogenase | Single protein | CESG, Center for Eukaryotic Structural Genomics. | Jr., G N.Phillips. | Kondrashov, D A. | Levin, E J. | Wesenberg, G E. | FAD | At5g21482 1 | Center for eukaryotic structural genomic | Cesg | Ckx | Cytokinin oxidase/dehydrogenase | Ensemble refinement | Oxidoreductase | Protein structure initiative | Psi | Refinement methodology development | Structural genomic
