1wad: Difference between revisions

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-{{Seed}}
-[[Image:1wad.png|left|200px]]
-<!--
+==CYTOCHROME C3 WITH 4 HEME GROUPS AND ONE CALCIUM ION==
-The line below this paragraph, containing "STRUCTURE_1wad", creates the "Structure Box" on the page.
+<StructureSection load='1wad' size='340' side='right'caption='[[1wad]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1wad]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Megalodesulfovibrio_gigas Megalodesulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WAD FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-{{STRUCTURE_1wad|  PDB=1wad  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wad OCA], [https://pdbe.org/1wad PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wad RCSB], [https://www.ebi.ac.uk/pdbsum/1wad PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wad ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CYC3_MEGG1 CYC3_MEGG1] Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.
+== 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/wa/1wad_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=1wad ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Crystals of the tetraheme cytochrome c3 from sulfate-reducing bacteria Desulfovibrio gigas (Dg) (MW 13 kDa, 111 residues, four heme groups) were obtained and X-ray diffraction data collected to 1.8 A resolution. The structure was solved by the method of molecular replacement and the resulting model refined to a conventional R-factor of 14.9%. The three-dimensional structure shows many similarities to other known crystal structures of tetraheme c3 cytochromes, but it also shows some remarkable differences. In particular, the location of the aromatic residues around the heme groups, which may play a fundamental role in the electron transfer processes of the molecule, are well conserved in the cases of hemes I, III, and IV. However, heme II has an aromatic environment that is completely different to that found in other related cytochromes c3. Another unusual feature is the presence of a Ca2+ ion coordinated by oxygen atoms supplied by the protein within a loop near the N-terminus. It is speculated that this loop may be stabilized by the presence of this Ca2+ ion, may contribute to heme-redox perturbation, and might even be involved in the specificity of recognition with its redox partner.
-===CYTOCHROME C3 WITH 4 HEME GROUPS AND ONE CALCIUM ION===
+Cytochrome c3 from Desulfovibrio gigas: crystal structure at 1.8 A resolution and evidence for a specific calcium-binding site.,Matias PM, Morais J, Coelho R, Carrondo MA, Wilson K, Dauter Z, Sieker L Protein Sci. 1996 Jul;5(7):1342-54. PMID:8819167<ref>PMID:8819167</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1wad" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_8819167}}, adds the Publication Abstract to the page
+*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 8819167 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_8819167}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-WAD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WAD OCA].
+[[Category: Megalodesulfovibrio gigas]]
+[[Category: Carrondo MA]]
-==Reference==
+[[Category: Coelho R]]
-Cytochrome c3 from Desulfovibrio gigas: crystal structure at 1.8 A resolution and evidence for a specific calcium-binding site., Matias PM, Morais J, Coelho R, Carrondo MA, Wilson K, Dauter Z, Sieker L, Protein Sci. 1996 Jul;5(7):1342-54. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8819167 8819167]
+[[Category: Dauter Z]]
-[[Category: Desulfovibrio gigas]]
+[[Category: Matias PM]]
-[[Category: Single protein]]
+[[Category: Morais J]]
-[[Category: Carrondo, M A.]]
+[[Category: Sieker L]]
-[[Category: Coelho, R.]]
+[[Category: Wilson K]]
-[[Category: Dauter, Z.]]
-[[Category: Matias, P M.]]
-[[Category: Morais, J.]]
-[[Category: Sieker, L.]]
-[[Category: Wilson, K.]]
-[[Category: Calcium binding]]
-[[Category: Electron transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 05:24:46 2008''