2q51
From Proteopedia
(New page: 200px<br /> <applet load="2q51" size="450" color="white" frame="true" align="right" spinBox="true" caption="2q51, resolution 2.800Å" /> '''Ensemble refinemen...) |
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| - | [[Image:2q51. | + | [[Image:2q51.jpg|left|200px]]<br /><applet load="2q51" size="350" color="white" frame="true" align="right" spinBox="true" |
| - | <applet load="2q51" size=" | + | |
caption="2q51, resolution 2.800Å" /> | caption="2q51, resolution 2.800Å" /> | ||
'''Ensemble refinement of the protein crystal structure of an aspartoacylase from Homo sapiens'''<br /> | '''Ensemble refinement of the protein crystal structure of an aspartoacylase from Homo sapiens'''<br /> | ||
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==Overview== | ==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. | 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. | ||
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| - | ==Disease== | ||
| - | Known diseases associated with this structure: Canavan disease OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=608034 608034]] | ||
==About this Structure== | ==About this Structure== | ||
| - | 2Q51 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with ZN and PO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Aspartoacylase Aspartoacylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.15 3.5.1.15] Full crystallographic information is available from [http:// | + | 2Q51 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=PO4:'>PO4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Aspartoacylase Aspartoacylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.15 3.5.1.15] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q51 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: zinc-dependent hydrolase]] | [[Category: zinc-dependent hydrolase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 13:08:14 2008'' |
Revision as of 11:08, 23 January 2008
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Ensemble refinement of the protein crystal structure of an aspartoacylase from Homo sapiens
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
2Q51 is a Single protein structure of sequence from Homo sapiens with and as ligands. Active as Aspartoacylase, with EC number 3.5.1.15 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 Wed Jan 23 13:08:14 2008
Categories: Aspartoacylase | Homo sapiens | Single protein | CESG, Center.for.Eukaryotic.Structural.Genomics. | Jr., G.N.Phillips. | Kondrashov, D.A. | Levin, E.J. | Wesenberg, G.E. | PO4 | ZN | Acy2 | Aminoacylase-2 | Aspa | Aspartoacylase family | Canavan disease | Center for eukaryotic structural genomics | Cesg | Ensemble refinement | N-acetyl-l-aspartate | Protein structure initiative | Psi | Refinement methodology development | Structural genomics | Zinc-dependent hydrolase
