2q4z

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{{Seed}}
 
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[[Image:2q4z.png|left|200px]]
 
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==Ensemble refinement of the protein crystal structure of an aspartoacylase from Rattus norvegicus==
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The line below this paragraph, containing "STRUCTURE_2q4z", creates the "Structure Box" on the page.
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<StructureSection load='2q4z' size='340' side='right'caption='[[2q4z]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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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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or leave the SCENE parameter empty for the default display.
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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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{{STRUCTURE_2q4z| PDB=2q4z | SCENE= }}
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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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===Ensemble refinement of the protein crystal structure of an aspartoacylase from Rattus norvegicus===
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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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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2q4z" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_17850744}}, adds the Publication Abstract to the page
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*[[Aminoacylase 3D structures|Aminoacylase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 17850744 is the PubMed ID number.
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*[[Aspartoacylase 3D structures|Aspartoacylase 3D structures]]
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== References ==
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{{ABSTRACT_PUBMED_17850744}}
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<references/>
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__TOC__
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==About this Structure==
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</StructureSection>
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2Q4Z is a [[Single protein]] structure of sequence from [http://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].
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[[Category: Large Structures]]
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==Reference==
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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://www.ncbi.nlm.nih.gov/pubmed/17850744 17850744]
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Structure of aspartoacylase, the brain enzyme impaired in Canavan disease., Bitto E, Bingman CA, Wesenberg GE, McCoy JG, Phillips GN Jr, Proc Natl Acad Sci U S A. 2007 Jan 9;104(2):456-61. Epub 2006 Dec 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17194761 17194761]
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[[Category: Aspartoacylase]]
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[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
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[[Category: Single protein]]
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[[Category: Kondrashov DA]]
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[[Category: CESG, Center for Eukaryotic Structural Genomics.]]
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[[Category: Levin EJ]]
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[[Category: Jr., G N.Phillips.]]
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[[Category: Phillips Jr GN]]
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[[Category: Kondrashov, D A.]]
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[[Category: Wesenberg GE]]
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[[Category: Levin, E J.]]
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[[Category: Wesenberg, G E.]]
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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 genomic]]
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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 genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 05:18:04 2008''
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Current revision

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

PDB ID 2q4z

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