1dqi: Difference between revisions

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 == Structural highlights ==
 <table><tr><td colspan='2'>[[1dqi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DQI FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</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]] 1.7&#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;'>[[1do6|1do6]], [[1dqk|1dqk]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</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=1dqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dqi OCA], [https://pdbe.org/1dqi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dqi RCSB], [https://www.ebi.ac.uk/pdbsum/1dqi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dqi ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/SOR_PYRFU SOR_PYRFU]] Uses electrons from reduced NADP, by way of rubredoxin and an oxidoreductase, to catalyze the reduction of superoxide to hydrogen peroxide.
+[https://www.uniprot.org/uniprot/SOR_PYRFU SOR_PYRFU] Uses electrons from reduced NADP, by way of rubredoxin and an oxidoreductase, to catalyze the reduction of superoxide to hydrogen peroxide.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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 </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=1dqi ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Superoxide reductase (SOR) is a blue non-heme iron protein that functions in anaerobic microbes as a defense mechanism against reactive oxygen species by catalyzing the reduction of superoxide to hydrogen peroxide [Jenney, F. E., Jr., Verhagen, M. F. J. M., Cui, X. , and Adams, M. W. W. (1999) Science 286, 306-309]. Crystal structures of SOR from the hyperthermophilic archaeon Pyrococcus furiosus have been determined in the oxidized and reduced forms to resolutions of 1.7 and 2.0 A, respectively. SOR forms a homotetramer, with each subunit adopting an immunoglobulin-like beta-barrel fold that coordinates a mononuclear, non-heme iron center. The protein fold and metal center are similar to those observed previously for the homologous protein desulfoferrodoxin from Desulfovibrio desulfuricans [Coelho, A. V., Matias, P., Fulop, V., Thompson, A., Gonzalez, A., and Carrondo, M. A. (1997) J. Bioinorg. Chem. 2, 680-689]. Each iron is coordinated to imidazole nitrogens of four histidines in a planar arrangement, with a cysteine ligand occupying an axial position normal to this plane. In two of the subunits of the oxidized structure, a glutamate carboxylate serves as the sixth ligand to form an overall six-coordinate, octahedral coordinate environment. In the remaining two subunits, the sixth coordination site is either vacant or occupied by solvent molecules. The iron centers in all four subunits of the reduced structure exhibit pentacoordination. The structures of the oxidized and reduced forms of SOR suggest a mechanism by which superoxide accessibility may be controlled and define a possible binding site for rubredoxin, the likely physiological electron donor to SOR.
-Structures of the superoxide reductase from Pyrococcus furiosus in the oxidized and reduced states.,Yeh AP, Hu Y, Jenney FE Jr, Adams MW, Rees DC Biochemistry. 2000 Mar 14;39(10):2499-508. PMID:10704199<ref>PMID:10704199</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1dqi" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Superoxide Reductase|Superoxide Reductase]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
 [[Category: Pyrococcus furiosus]]
-[[Category: Adams, M W.W]]
+[[Category: Adams MWW]]
-[[Category: Hu, Y]]
+[[Category: Hu Y]]
-[[Category: Jenney, F E]]
+[[Category: Jenney Jr FE]]
-[[Category: Rees, D C]]
+[[Category: Rees DC]]
-[[Category: Yeh, A P]]
+[[Category: Yeh AP]]
-[[Category: Non-heme iron protein]]
-[[Category: Oxidoreductase]]