2q4z

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[[Image:2q4z.jpg|left|200px]]
[[Image:2q4z.jpg|left|200px]]
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{{Structure
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<!--
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|PDB= 2q4z |SIZE=350|CAPTION= <scene name='initialview01'>2q4z</scene>, resolution 1.800&Aring;
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The line below this paragraph, containing "STRUCTURE_2q4z", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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|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>
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or leave the SCENE parameter empty for the default display.
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|GENE= Aspa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus])
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-->
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|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK02259 PRK02259]</span>
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{{STRUCTURE_2q4z| PDB=2q4z | SCENE= }}
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|RELATEDENTRY=[[2gu2|2GU2]], [[2i3c|2I3C]]
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|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.rcsb.org/pdb/explore.do?structureId=2q4z RCSB]</span>
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}}
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'''Ensemble refinement of the protein crystal structure of an aspartoacylase from Rattus norvegicus'''
'''Ensemble refinement of the protein crystal structure of an aspartoacylase from Rattus norvegicus'''
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[[Category: Levin, E J.]]
[[Category: Levin, E J.]]
[[Category: Wesenberg, G E.]]
[[Category: Wesenberg, G E.]]
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[[Category: acy-2]]
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[[Category: Acy-2]]
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[[Category: acy2_rat]]
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[[Category: Acy2_rat]]
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[[Category: aminoacylase-2]]
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[[Category: Aminoacylase-2]]
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[[Category: aspartoacylase family]]
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[[Category: Aspartoacylase family]]
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[[Category: center for eukaryotic structural genomic]]
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[[Category: Center for eukaryotic structural genomic]]
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[[Category: cesg]]
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[[Category: Cesg]]
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[[Category: ensemble refinement]]
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[[Category: Ensemble refinement]]
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[[Category: hydrolase]]
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[[Category: Hydrolase]]
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[[Category: protein structure initiative]]
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[[Category: Protein structure initiative]]
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[[Category: psi]]
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[[Category: Psi]]
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[[Category: refinement methodology development]]
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[[Category: Refinement methodology development]]
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[[Category: structural genomic]]
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[[Category: Structural genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 14:21:58 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:44:50 2008''
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Revision as of 11:22, 4 May 2008

Image:2q4z.jpg

Template:STRUCTURE 2q4z

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 Sun May 4 14:21:58 2008

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OCA

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