2q3w: Difference between revisions
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New page: left|200px<br /><applet load="2q3w" size="450" color="white" frame="true" align="right" spinBox="true" caption="2q3w, resolution 1.480Å" /> '''Ensemble refinement... |
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== | ==Ensemble refinement of the protein crystal structure of the cys84ala cys85ala double mutant of the [2Fe-2S] ferredoxin subunit of toluene-4-monooxygenase from Pseudomonas mendocina KR1== | ||
X-ray crystallography typically uses a single set of coordinates and B | <StructureSection load='2q3w' size='340' side='right'caption='[[2q3w]], [[Resolution|resolution]] 1.48Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2q3w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_mendocina Pseudomonas mendocina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q3W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q3W 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]] 1.48Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=2q3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3w OCA], [https://pdbe.org/2q3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q3w RCSB], [https://www.ebi.ac.uk/pdbsum/2q3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q3w ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/TMOC_ECTME TMOC_ECTME] Ferredoxin component of the toluene-4-monooxygenase multicomponent enzyme system which catalyzes the O2- and NADH-dependent hydroxylation of toluene to form p-cresol (PubMed:15240250, PubMed:1885512). Functions as an intermediate electron transfer protein (PubMed:15240250).<ref>PMID:15240250</ref> <ref>PMID:1885512</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/q3/2q3w_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=2q3w 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> | |||
== | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | |||
<div class="pdbe-citations 2q3w" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Ferredoxin 3D structures|Ferredoxin 3D structures]] | |||
*[[Monooxygenase 3D structures|Monooxygenase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Pseudomonas mendocina]] | [[Category: Pseudomonas mendocina]] | ||
[[Category: | [[Category: Kondrashov DA]] | ||
[[Category: | [[Category: Levin EJ]] | ||
[[Category: Jr | [[Category: Phillips Jr GN]] | ||
[[Category: Wesenberg GE]] | |||
[[Category: Wesenberg | |||
Latest revision as of 08:30, 13 August 2026
Ensemble refinement of the protein crystal structure of the cys84ala cys85ala double mutant of the [2Fe-2S] ferredoxin subunit of toluene-4-monooxygenase from Pseudomonas mendocina KR1
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