2q4z

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(New page: 200px<br /><applet load="2q4z" size="450" color="white" frame="true" align="right" spinBox="true" caption="2q4z, resolution 1.800&Aring;" /> '''Ensemble refinement...)
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[[Image:2q4z.jpg|left|200px]]<br /><applet load="2q4z" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2q4z, resolution 1.800&Aring;" />
 
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'''Ensemble refinement of the protein crystal structure of an aspartoacylase from Rattus norvegicus'''<br />
 
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==Overview==
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==Ensemble refinement of the protein crystal structure of an aspartoacylase from Rattus norvegicus==
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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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<StructureSection load='2q4z' size='340' side='right'caption='[[2q4z]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2q4z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4Z FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;, 16 models</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4z OCA], [https://pdbe.org/2q4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4z RCSB], [https://www.ebi.ac.uk/pdbsum/2q4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4z ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/ACY2_RAT ACY2_RAT] Catalyzes the deacetylation of N-acetylaspartic acid (NAA) to produce acetate and L-aspartate. NAA occurs in high concentration in brain and its hydrolysis NAA plays a significant part in the maintenance of intact white matter (By similarity).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q4/2q4z_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2q4z ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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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==About this Structure==
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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<ref>PMID:17850744</ref>
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2Q4Z is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with ZN and SO4 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=2Q4Z OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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]
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</div>
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[[Category: Aspartoacylase]]
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<div class="pdbe-citations 2q4z" style="background-color:#fffaf0;"></div>
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[[Category: Rattus norvegicus]]
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[[Category: Single protein]]
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[[Category: CESG, Center.for.Eukaryotic.Structural.Genomics.]]
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[[Category: Jr., G.N.Phillips.]]
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[[Category: Kondrashov, D.A.]]
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[[Category: Levin, E.J.]]
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[[Category: Wesenberg, G.E.]]
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[[Category: SO4]]
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[[Category: ZN]]
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[[Category: acy-2]]
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[[Category: acy2_rat]]
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[[Category: aminoacylase-2]]
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[[Category: aspartoacylase family]]
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[[Category: center for eukaryotic structural genomics]]
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[[Category: cesg]]
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[[Category: ensemble refinement]]
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[[Category: hydrolase]]
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[[Category: protein structure initiative]]
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[[Category: psi]]
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[[Category: refinement methodology development]]
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[[Category: structural genomics]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 13:49:13 2007''
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==See Also==
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*[[Aminoacylase 3D structures|Aminoacylase 3D structures]]
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*[[Aspartoacylase 3D structures|Aspartoacylase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Rattus norvegicus]]
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[[Category: Kondrashov DA]]
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[[Category: Levin EJ]]
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[[Category: Phillips Jr GN]]
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[[Category: Wesenberg GE]]

Current revision

Ensemble refinement of the protein crystal structure of an aspartoacylase from Rattus norvegicus

PDB ID 2q4z

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