3ixf: Difference between revisions

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-{{Seed}}
-[[Image:3ixf.jpg|left|200px]]
-<!--
+==Crystal Structure of Dehaloperoxidase B at 1.58 and Structural Characterization of the AB Dimer from Amphitrite ornata==
-The line below this paragraph, containing "STRUCTURE_3ixf", creates the "Structure Box" on the page.
+<StructureSection load='3ixf' size='340' side='right'caption='[[3ixf]], [[Resolution|resolution]] 1.58&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'>[[3ixf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IXF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IXF 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]] 1.58&#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=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3ixf|  PDB=3ixf  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ixf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ixf OCA], [https://pdbe.org/3ixf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ixf RCSB], [https://www.ebi.ac.uk/pdbsum/3ixf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ixf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9NAV7_9ANNE Q9NAV7_9ANNE]
+== 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/ix/3ixf_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=3ixf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+As members of the globin superfamily, dehaloperoxidase (DHP) isoenzymes A and B from the marine annelid Amphitrite ornata possess hemoglobin function, but they also exhibit a biologically relevant peroxidase activity that is capable of converting 2,4,6-trihalophenols to the corresponding 2,6-dihaloquinones in the presence of hydrogen peroxide. Here, a comprehensive structural study of recombinant DHP B, both by itself and cocrystallized with isoenzyme A, using X-ray diffraction is presented. The structure of DHP B refined to 1.58 A resolution exhibits the same distal histidine (His55) conformational flexibility as that observed in isoenzyme A, as well as additional changes to the distal and proximal hydrogen-bonding networks. Furthermore, preliminary characterization of the DHP AB heterodimer is presented, which exhibits differences in the AB interface that are not observed in the A-only or B-only homodimers. These structural investigations of DHP B provide insights that may relate to the mechanistic details of the H(2)O(2)-dependent oxidative dehalogenation reaction catalyzed by dehaloperoxidase, present a clearer description of the function of specific residues in DHP at the molecular level and lead to a better understanding of the paradigms of globin structure-function relationships.
-===Crystal Structure of Dehaloperoxidase B at 1.58 and Structural Characterization of the AB Dimer from Amphitrite ornata===
+Structure of dehaloperoxidase B at 1.58 A resolution and structural characterization of the AB dimer from Amphitrite ornata.,de Serrano V, D'Antonio J, Franzen S, Ghiladi RA Acta Crystallogr D Biol Crystallogr. 2010 May;66(Pt 5):529-38. Epub 2010, Apr 21. PMID:20445228<ref>PMID:20445228</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3ixf" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20445228}}, adds the Publication Abstract to the page
+*[[Dehaloperoxidase 3D structures|Dehaloperoxidase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20445228 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20445228}}
+__TOC__
+</StructureSection>
-==About this Structure==
-IXF is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IXF OCA].
-==Reference==
-<ref group="xtra">PMID:20445228</ref><references group="xtra"/>
 [[Category: Amphitrite ornata]]
-[[Category: Antonio, J D.]]
+[[Category: Large Structures]]
-[[Category: Franzen, S.]]
+[[Category: D'Antonio J]]
-[[Category: Ghiladi, R A.]]
+[[Category: Franzen S]]
-[[Category: Serrano, V S.de.]]
+[[Category: Ghiladi RA]]
-[[Category: Thompson, M K.]]
+[[Category: Thompson MK]]
-[[Category: Globin]]
+[[Category: De Serrano VS]]
-[[Category: Heme]]
-[[Category: Oxidoreductase]]
-[[Category: Oxygen transport]]
-[[Category: Peroxidase]]
-[[Category: Transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu May 20 09:32:46 2010''