2q4c
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| - | [[Image:2q4c.jpg|left|200px]]<br /><applet load="2q4c" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="2q4c, resolution 2.508Å" /> | ||
| - | '''Ensemble refinement of the protein crystal structure of annexin from Arabidopsis thaliana gene At1g35720'''<br /> | ||
| - | == | + | ==Ensemble refinement of the protein crystal structure of annexin from Arabidopsis thaliana gene At1g35720== |
| - | X-ray crystallography typically uses a single set of coordinates and B | + | <StructureSection load='2q4c' size='340' side='right'caption='[[2q4c]], [[Resolution|resolution]] 2.51Å' scene=''> |
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[2q4c]] 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=2Q4C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4C FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.508Å</td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q4c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4c OCA], [https://pdbe.org/2q4c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4c RCSB], [https://www.ebi.ac.uk/pdbsum/2q4c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4c ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/ANXD1_ARATH ANXD1_ARATH] Has a peroxidase activity. May act in counteracting oxidative stress. May also mediate regulated, targeted secretion of Golgi-derived vesicles during seedling development.<ref>PMID:16153598</ref> <ref>PMID:15368128</ref> | ||
| + | == 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/q4/2q4c_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2q4c 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 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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 2q4c" style="background-color:#fffaf0;"></div> | |
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| - | + | ==See Also== | |
| + | *[[Annexin 3D structures|Annexin 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Arabidopsis thaliana]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Kondrashov DA]] | ||
| + | [[Category: Levin EJ]] | ||
| + | [[Category: Phillips Jr GN]] | ||
| + | [[Category: Wesenberg GE]] | ||
Current revision
Ensemble refinement of the protein crystal structure of annexin from Arabidopsis thaliana gene At1g35720
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