1dw2: Difference between revisions

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-[[Image:1dw2.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1dw2", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_1dw2|  PDB=1dw2  |  SCENE=  }}
-'''STRUCTURE OF THE NITRIC OXIDE COMPLEX OF REDUCED SHP, AN OXYGEN BINDING CYTOCHROME C'''
+==STRUCTURE OF THE NITRIC OXIDE COMPLEX OF REDUCED SHP, AN OXYGEN BINDING CYTOCHROME C==
+<StructureSection load='1dw2' size='340' side='right'caption='[[1dw2]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1dw2]] 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=1DW2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DW2 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]] 2.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NO:NITRIC+OXIDE'>NO</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=1dw2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw2 OCA], [https://pdbe.org/1dw2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dw2 RCSB], [https://www.ebi.ac.uk/pdbsum/1dw2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dw2 ProSAT]</span></td></tr>
+</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 minutes 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/1dw2_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=1dw2 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.
-==Overview==
+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>
-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.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-DW2 is a [[Single protein]] structure of 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=1DW2 OCA].
+</div>
+<div class="pdbe-citations 1dw2" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-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:[http://www.ncbi.nlm.nih.gov/pubmed/10821858 10821858]
+*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
-[[Category: Rhodobacter sphaeroides]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Backers, K.]]
+__TOC__
-[[Category: Beeumen, J J.Van.]]
+</StructureSection>
-[[Category: Cusanovich, M A.]]
+[[Category: Cereibacter sphaeroides]]
-[[Category: Hagen, W R.]]
+[[Category: Large Structures]]
-[[Category: Leys, D.]]
+[[Category: Backers K]]
-[[Category: Meyer, T E.]]
+[[Category: Cusanovich MA]]
-[[Category: Asparagine ligation]]
+[[Category: Hagen WR]]
-[[Category: Cytochrome c]]
+[[Category: Leys D]]
-[[Category: Disulfide bridge]]
+[[Category: Meyer TE]]
-[[Category: Nitric oxide]]
+[[Category: Van Beeumen JJ]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 14:21:05 2008''