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2q3w

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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

Structural highlights

2q3w is a 1 chain structure with sequence from Pseudomonas mendocina. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.48Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TMOC_PSEME Probable electron transfer from NADPH, via FAD and the 2Fe-2S center, to the oxygenase activity site of the enzyme.

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 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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr. Ensemble refinement of protein crystal structures: validation and application. Structure. 2007 Sep;15(9):1040-52. PMID:17850744 doi:http://dx.doi.org/10.1016/j.str.2007.06.019

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2q3w"

@@ Line 3: / Line 3: @@
 <StructureSection load='2q3w' size='340' side='right'caption='[[2q3w]], [[Resolution|resolution]] 1.48&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2q3w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_25411 Atcc 25411]. 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>
+<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='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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.48&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1vm9|1vm9]]</div></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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tmoC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300 ATCC 25411])</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_PSEME TMOC_PSEME]] Probable electron transfer from NADPH, via FAD and the 2Fe-2S center, to the oxygenase activity site of the enzyme.
+[https://www.uniprot.org/uniprot/TMOC_PSEME TMOC_PSEME] Probable electron transfer from NADPH, via FAD and the 2Fe-2S center, to the oxygenase activity site of the enzyme.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 38: / Line 37: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 25411]]
 [[Category: Large Structures]]
-[[Category: Structural genomic]]
+[[Category: Pseudomonas mendocina]]
-[[Category: Kondrashov, D A]]
+[[Category: Kondrashov DA]]
-[[Category: Levin, E J]]
+[[Category: Levin EJ]]
-[[Category: Phillips, G N]]
+[[Category: Phillips Jr GN]]
-[[Category: Wesenberg, G E]]
+[[Category: Wesenberg GE]]
-[[Category: Cesg]]
-[[Category: Electron transport]]
-[[Category: Ensemble refinement]]
-[[Category: Fe]]
-[[Category: Ferredoxin]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Refinement methodology development]]
-[[Category: Rieske protein]]
-[[Category: Toluene-4-monooxygenase subunit]]

2q3w

From Proteopedia

Current revision

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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