2q4e: Difference between revisions

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-{{Seed}}
-[[Image:2q4e.png|left|200px]]
-<!--
+==Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At4g09670==
-The line below this paragraph, containing "STRUCTURE_2q4e", creates the "Structure Box" on the page.
+<StructureSection load='2q4e' size='340' side='right'caption='[[2q4e]], [[Resolution|resolution]] 2.49&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2q4e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4E FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.49&#8491;, 16 models</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_2q4e|  PDB=2q4e  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4e OCA], [https://pdbe.org/2q4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4e RCSB], [https://www.ebi.ac.uk/pdbsum/2q4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4e ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Y4967_ARATH Y4967_ARATH]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q4/2q4e_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=2q4e ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-===Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At4g09670===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_17850744}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2q4e" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17850744 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17850744}}
+__TOC__
+</StructureSection>
-==About this Structure==
-Q4E is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4E OCA].
-==Reference==
-<ref group="xtra">PMID:17850744</ref><references group="xtra"/>
 [[Category: Arabidopsis thaliana]]
-[[Category: CESG, Center for Eukaryotic Structural Genomics.]]
+[[Category: Large Structures]]
-[[Category: Jr., G N.Phillips.]]
+[[Category: Kondrashov DA]]
-[[Category: Kondrashov, D A.]]
+[[Category: Levin EJ]]
-[[Category: Levin, E J.]]
+[[Category: Phillips Jr GN]]
-[[Category: Wesenberg, G E.]]
+[[Category: Wesenberg GE]]
-[[Category: At4g09670]]
-[[Category: Center for eukaryotic structural genomic]]
-[[Category: Cesg]]
-[[Category: Ensemble refinement]]
-[[Category: Oxidoreductase]]
-[[Category: Protein structure initiative]]
-[[Category: Psi]]
-[[Category: Refinement methodology development]]
-[[Category: Structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:27:50 2009''