1t6q: Difference between revisions

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-{{Seed}}
-[[Image:1t6q.png|left|200px]]
-<!--
+==Nickel Superoxide Dismutase (NiSOD) CN-treated Apo Structure==
-The line below this paragraph, containing "STRUCTURE_1t6q", creates the "Structure Box" on the page.
+<StructureSection load='1t6q' size='340' side='right'caption='[[1t6q]], [[Resolution|resolution]] 2.05&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'>[[1t6q]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_coelicolor Streptomyces coelicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T6Q 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]] 2.05&#8491;</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=1t6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6q OCA], [https://pdbe.org/1t6q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t6q RCSB], [https://www.ebi.ac.uk/pdbsum/1t6q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6q ProSAT]</span></td></tr>
-{{STRUCTURE_1t6q|  PDB=1t6q  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SODN_STRCO SODN_STRCO]
+== 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/t6/1t6q_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/main_output.php?pdb_ID=1t6q ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The 1.30 A resolution crystal structure of nickel superoxide dismutase (NiSOD) identifies a novel SOD fold, assembly, and Ni active site. NiSOD is a hexameric assembly of right-handed 4-helix bundles of up-down-up-down topology with N-terminal hooks chelating the active site Ni ions. This newly identified nine-residue Ni-hook structural motif (His-Cys-X-X-Pro-Cys-Gly-X-Tyr) provides almost all interactions critical for metal binding and catalysis, and thus will likely be diagnostic of NiSODs. Conserved lysine residues are positioned for electrostatic guidance of the superoxide anion to the narrow active site channel. Apo structures show that the Ni-hook motif is unfolded prior to metal binding. The active site Ni geometry cycles from square planar Ni(II), with thiolate (Cys2 and Cys6) and backbone nitrogen (His1 and Cys2) ligands, to square pyramidal Ni(III) with an added axial His1 side chain ligand, consistent with electron paramagentic resonance spectroscopy. Analyses of the three NiSOD structures and comparisons to the Cu,Zn and Mn/Fe SODs support specific molecular mechanisms for NiSOD maturation and catalysis, and identify important structure-function relationships conserved among SODs.
-===Nickel Superoxide Dismutase (NiSOD) CN-treated Apo Structure===
+Nickel superoxide dismutase structure and mechanism.,Barondeau DP, Kassmann CJ, Bruns CK, Tainer JA, Getzoff ED Biochemistry. 2004 Jun 29;43(25):8038-47. PMID:15209499<ref>PMID:15209499</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1t6q" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15209499}}, adds the Publication Abstract to the page
+*[[Superoxide dismutase 3D structures|Superoxide dismutase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15209499 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15209499}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-T6Q is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Streptomyces_coelicolor Streptomyces coelicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6Q OCA].
-==Reference==
-<ref group="xtra">PMID:15209499</ref><references group="xtra"/>
 [[Category: Streptomyces coelicolor]]
-[[Category: Superoxide dismutase]]
+[[Category: Barondeau DP]]
-[[Category: Barondeau, D P.]]
+[[Category: Bruns CK]]
-[[Category: Bruns, C K.]]
+[[Category: Getzoff ED]]
-[[Category: Getzoff, E D.]]
+[[Category: Kassmann CJ]]
-[[Category: Kassmann, C J.]]
+[[Category: Tainer JA]]
-[[Category: Tainer, J A.]]
-[[Category: 4-helix bundle]]
-[[Category: Apo]]
-[[Category: Cyanide]]
-[[Category: Hexamer]]
-[[Category: Nickel]]
-[[Category: Nisod]]
-[[Category: Sod]]
-[[Category: Superoxide dismutase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 05:25:43 2009''