1dw3: Difference between revisions

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 ==STRUCTURE OF A REDUCED OXYGEN BINDING CYTOCHROME C==
-<StructureSection load='1dw3' size='340' side='right' caption='[[1dw3]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='1dw3' size='340' side='right'caption='[[1dw3]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1dw3]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DW3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1dw3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Cereibacter_sphaeroides Cereibacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DW3 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><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]] 2.1&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dw0|1dw0]], [[1dw1|1dw1]], [[1dw2|1dw2]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dw3 RCSB], [http://www.ebi.ac.uk/pdbsum/1dw3 PDBsum]</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=1dw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw3 OCA], [https://pdbe.org/1dw3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dw3 RCSB], [https://www.ebi.ac.uk/pdbsum/1dw3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dw3 ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SHP_CERS4 SHP_CERS4] High-spin cytochrome. Transiently bind oxygen during autoxidation, which occurs with a half-life of 3 min with a 4-fold excess of O(2). Also binds carbon monoxide, azide and cyanide.
 == 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/dw/1dw3_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dw/1dw3_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1dw3 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The photosynthetic bacterium Rhodobacter sphaeroides produces a heme protein (SHP), which is an unusual c-type cytochrome capable of transiently binding oxygen during autooxidation. Similar proteins have not only been observed in other photosynthetic bacteria but also in the obligate methylotroph Methylophilus methylotrophus and the metal reducing bacterium Shewanella putrefaciens. A three-dimensional structure of SHP was derived using the multiple isomorphous replacement phasing method. Besides a model for the oxidized state (to 1.82 A resolution), models for the reduced state (2.1 A resolution), the oxidized molecule liganded with cyanide (1. 90 A resolution), and the reduced molecule liganded with nitric oxide (2.20 A resolution) could be derived. The SHP structure represents a new variation of the class I cytochrome c fold. The oxidized state reveals a novel sixth heme ligand, Asn(88), which moves away from the iron upon reduction or when small molecules bind. The distal side of the heme has a striking resemblance to other heme proteins that bind gaseous compounds. In SHP the liberated amide group of Asn(88) stabilizes solvent-shielded ligands through a hydrogen bond.
-Crystal structures of an oxygen-binding cytochrome c from Rhodobacter sphaeroides.,Leys D, Backers K, Meyer TE, Hagen WR, Cusanovich MA, Van Beeumen JJ J Biol Chem. 2000 May 26;275(21):16050-6. PMID:10821858<ref>PMID:10821858</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Cytochrome c|Cytochrome c]]
+*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Rhodobacter sphaeroides]]
+[[Category: Cereibacter sphaeroides]]
-[[Category: Backers, K.]]
+[[Category: Large Structures]]
-[[Category: Beeumen, J J.Van.]]
+[[Category: Backers K]]
-[[Category: Cusanovich, M A.]]
+[[Category: Cusanovich MA]]
-[[Category: Hagen, W R.]]
+[[Category: Hagen WR]]
-[[Category: Leys, D.]]
+[[Category: Leys D]]
-[[Category: Meyer, T E.]]
+[[Category: Meyer TE]]
-[[Category: Asparagine ligation]]
+[[Category: Van Beeumen JJ]]
-[[Category: Cytochrome c]]
-[[Category: Disulfide bridge]]
-[[Category: Oxygen storage-transport complex]]
-[[Category: Reduced]]