2q4r
From Proteopedia
(New page: 200px<br /> <applet load="2q4r" size="450" color="white" frame="true" align="right" spinBox="true" caption="2q4r, resolution 2.090Å" /> '''Ensemble refinemen...) |
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caption="2q4r, resolution 2.090Å" /> | caption="2q4r, resolution 2.090Å" /> | ||
'''Ensemble refinement of the protein crystal structure of human phosphomannomutase 2 (PMM2)'''<br /> | '''Ensemble refinement of the protein crystal structure of human phosphomannomutase 2 (PMM2)'''<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 disease associated with this structure: Carbohydrate-deficient glycoprotein syndrome, type I OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=601785 601785]] | ||
==About this Structure== | ==About this Structure== | ||
| - | 2Q4R 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 EDO and GLY as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Phosphomannomutase Phosphomannomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.8 5.4.2.8] Full crystallographic information is available from [http:// | + | 2Q4R 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=EDO:'>EDO</scene> and <scene name='pdbligand=GLY:'>GLY</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Phosphomannomutase Phosphomannomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.8 5.4.2.8] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4R OCA]. |
==Reference== | ==Reference== | ||
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[[Category: structural genomics]] | [[Category: structural genomics]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 13:07:59 2008'' |
Revision as of 11:07, 23 January 2008
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Ensemble refinement of the protein crystal structure of human phosphomannomutase 2 (PMM2)
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
2Q4R is a Single protein structure of sequence from Homo sapiens with and as ligands. Active as Phosphomannomutase, with EC number 5.4.2.8 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 13:07:59 2008
Categories: Homo sapiens | Phosphomannomutase | Single protein | CESG, Center.for.Eukaryotic.Structural.Genomics. | Jr., G.N.Phillips. | Kondrashov, D.A. | Levin, E.J. | Wesenberg, G.E. | EDO | GLY | Bc008310 | Carbohydrate-deficient glycoprotein syndrome | Center for eukaryotic structural genomics | Cesg | Ensemble refinement | Had superfamily | Hs.313504 | Hs.459855 | Isomerase | Jaecken disease | Pfam pf03332 | Phosphatase | Protein structure initiative | Psi | Refinement methodology development | Structural genomics
