2q52: Difference between revisions
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<StructureSection load='2q52' size='340' side='right' caption='[[2q52]], [[Resolution|resolution]] 1.38Å' scene=''> | <StructureSection load='2q52' size='340' side='right' caption='[[2q52]], [[Resolution|resolution]] 1.38Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2q52]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Galdieria_sulphuraria Galdieria sulphuraria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q52 OCA]. <br> | <table><tr><td colspan='2'>[[2q52]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Galdieria_sulphuraria Galdieria sulphuraria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q52 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q52 FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2i3f|2i3f]]</td></tr> | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2i3f|2i3f]]</td></tr> | ||
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">c503_101305g25.t1, MSU_Galdi ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=130081 Galdieria sulphuraria])</td></tr> | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">c503_101305g25.t1, MSU_Galdi ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=130081 Galdieria sulphuraria])</td></tr> | ||
<tr | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q52 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q52 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q52 RCSB], [http://www.ebi.ac.uk/pdbsum/2q52 PDBsum]</span></td></tr> | ||
</table> | |||
<table> | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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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> | 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 | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
== References == | == References == | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Galdieria sulphuraria]] | [[Category: Galdieria sulphuraria]] | ||
[[Category: | [[Category: Structural genomic]] | ||
[[Category: Kondrashov, D A | [[Category: Kondrashov, D A]] | ||
[[Category: Levin, E J | [[Category: Levin, E J]] | ||
[[Category: Phillips, G N | [[Category: Phillips, G N]] | ||
[[Category: Wesenberg, G E | [[Category: Wesenberg, G E]] | ||
[[Category: Cesg]] | [[Category: Cesg]] | ||
[[Category: Ensemble refinement]] | [[Category: Ensemble refinement]] | ||
[[Category: Gltp superfamily]] | [[Category: Gltp superfamily]] | ||
[[Category: Gltp-like]] | [[Category: Gltp-like]] | ||
[[Category: Protein structure initiative | [[Category: PSI, Protein structure initiative]] | ||
[[Category: Refinement methodology development]] | [[Category: Refinement methodology development]] | ||
[[Category: Unknown function]] | [[Category: Unknown function]] | ||
Revision as of 19:03, 24 December 2014
Ensemble refinement of the crystal structure of a glycolipid transfer-like protein from Galdieria sulphurariaEnsemble refinement of the crystal structure of a glycolipid transfer-like protein from Galdieria sulphuraria
Structural highlights
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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