2q4j: Difference between revisions
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<StructureSection load='2q4j' size='340' side='right'caption='[[2q4j]], [[Resolution|resolution]] 1.86Å' scene=''> | <StructureSection load='2q4j' size='340' side='right'caption='[[2q4j]], [[Resolution|resolution]] 1.86Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2q4j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[2q4j]] 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=2Q4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4J FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.863Å</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=2q4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4j OCA], [https://pdbe.org/2q4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4j RCSB], [https://www.ebi.ac.uk/pdbsum/2q4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4j ProSAT]</span></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=2q4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4j OCA], [https://pdbe.org/2q4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4j RCSB], [https://www.ebi.ac.uk/pdbsum/2q4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4j ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/UGPA2_ARATH UGPA2_ARATH] Plays a central role as a glucosyl donor in cellular metabolic pathways (By similarity). | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Arabidopsis thaliana]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Kondrashov DA]] | |||
[[Category: Levin EJ]] | |||
[[Category: Kondrashov | [[Category: Phillips Jr GN]] | ||
[[Category: Levin | [[Category: Wesenberg GE]] | ||
[[Category: Phillips | |||
[[Category: Wesenberg | |||
Latest revision as of 14:19, 30 August 2023
Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g03250, a putative UDP-glucose pyrophosphorylaseEnsemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g03250, a putative UDP-glucose pyrophosphorylase
Structural highlights
FunctionUGPA2_ARATH Plays a central role as a glucosyl donor in cellular metabolic pathways (By similarity). Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedX-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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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