2q4z
From Proteopedia
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|PDB= 2q4z |SIZE=350|CAPTION= <scene name='initialview01'>2q4z</scene>, resolution 1.800Å | |PDB= 2q4z |SIZE=350|CAPTION= <scene name='initialview01'>2q4z</scene>, resolution 1.800Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> |
| - | |ACTIVITY= [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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= Aspa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus]) | |GENE= Aspa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus]) | ||
| + | |DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK02259 PRK02259]</span> | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4z OCA], [http://www.ebi.ac.uk/pdbsum/2q4z PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=2q4z RCSB]</span> | ||
}} | }} | ||
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[[Category: Levin, E J.]] | [[Category: Levin, E J.]] | ||
[[Category: Wesenberg, G E.]] | [[Category: Wesenberg, G E.]] | ||
| - | [[Category: SO4]] | ||
| - | [[Category: ZN]] | ||
[[Category: acy-2]] | [[Category: acy-2]] | ||
[[Category: acy2_rat]] | [[Category: acy2_rat]] | ||
| Line 43: | Line 43: | ||
[[Category: structural genomic]] | [[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 Wed Mar 26 06:42:14 2008'' |
Revision as of 04:42, 26 March 2008
| |||||||
| , resolution 1.800Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | Aspa (Rattus norvegicus) | ||||||
| Activity: | Aspartoacylase, with EC number 3.5.1.15 | ||||||
| Domains: | PRK02259 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, JenaLib, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Ensemble refinement of the protein crystal structure of an aspartoacylase from Rattus norvegicus
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
2Q4Z is a Single protein structure of sequence from Rattus norvegicus. 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 Mar 26 06:42:14 2008
Categories: Aspartoacylase | Rattus norvegicus | Single protein | CESG, Center for Eukaryotic Structural Genomics. | Jr., G N.Phillips. | Kondrashov, D A. | Levin, E J. | Wesenberg, G E. | Acy-2 | Acy2 rat | Aminoacylase-2 | Aspartoacylase family | Center for eukaryotic structural genomic | Cesg | Ensemble refinement | Hydrolase | Protein structure initiative | Psi | Refinement methodology development | Structural genomic
