3eh3: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3eh3.jpg|left|200px]]
-<!--
+==Structure of the reduced form of cytochrome ba3 oxidase from Thermus thermophilus==
-The line below this paragraph, containing "STRUCTURE_3eh3", creates the "Structure Box" on the page.
+<StructureSection load='3eh3' size='340' side='right'caption='[[3eh3]], [[Resolution|resolution]] 3.10&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'>[[3eh3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EH3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EH3 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]] 3.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-{{STRUCTURE_3eh3|  PDB=3eh3  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3eh3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eh3 OCA], [https://pdbe.org/3eh3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eh3 RCSB], [https://www.ebi.ac.uk/pdbsum/3eh3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eh3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/COX1_THET8 COX1_THET8]
+== 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/eh/3eh3_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=3eh3 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Three paths for obtaining crystals of reduced (II-E4Q/I-K258R) cytochrome ba(3) are described, and the structures of these are reported at approximately 2.8-3.0 A resolution. Microspectrophotometry of single crystals of Thermus ba(3) oxidase at 100 K was used to show that crystals of the oxidized enzyme are reduced in an intense X-ray (beam line 7-1 at the Stanford Synchrotron Radiation Laboratory), being nearly complete in 1 min. The previously reported structures of ba(3) (Protein Data Bank entries 1EHK and 1XME ), having a crystallographically detectable water between the Cu(B) and Fe(a3) metals of the dinuclear center, actually represent the X-ray radiation-reduced enzyme. Dithionite-reduced crystals or crystals formed from dithionite-reduced enzyme revealed the absence of the above-mentioned water and an increase in the Cu(B)-Fe(a3) distance of approximately 0.3 A. The new structures are discussed in terms of enzyme function. An unexpected optical absorption envelope at approximately 590 nm is also reported. This spectral feature is tentatively thought to arise from a five-coordinate, low-spin, ferrous heme a(3) that is trapped in the frozen crystals.
-===Structure of the reduced form of cytochrome ba3 oxidase from Thermus thermophilus===
+Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the reduced form of the enzyme.,Liu B, Chen Y, Doukov T, Soltis SM, Stout CD, Fee JA Biochemistry. 2009 Feb 10;48(5):820-6. PMID:19140675<ref>PMID:19140675</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3eh3" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19140675}}, adds the Publication Abstract to the page
+*[[Cytochrome c oxidase 3D structures|Cytochrome c oxidase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19140675 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19140675}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-EH3 is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EH3 OCA].
+[[Category: Thermus thermophilus HB8]]
+[[Category: Chen Y]]
-==Reference==
+[[Category: Doukov T]]
-<ref group="xtra">PMID:19140675</ref><ref group="xtra">PMID:18084085</ref><ref group="xtra">PMID:15735345</ref><references group="xtra"/>
+[[Category: Fee JA]]
-[[Category: Cytochrome-c oxidase]]
+[[Category: Liu B]]
-[[Category: Thermus thermophilus hb8]]
+[[Category: Soltis SM]]
-[[Category: Chen,Y.]]
+[[Category: Stout D]]
-[[Category: Doukov,T.]]
-[[Category: Fee,J A.]]
-[[Category: Liu,B]]
-[[Category: Soltis,S M.]]
-[[Category: Stout,D.]]
-[[Category: Cell membrane]]
-[[Category: Copper]]
-[[Category: Cytochrome ba3 oxidase]]
-[[Category: Electron transport]]
-[[Category: Formylation]]
-[[Category: Heme]]
-[[Category: Hydrogen ion transport]]
-[[Category: Integral membrane protein]]
-[[Category: Ion transport]]
-[[Category: Iron]]
-[[Category: Membrane]]
-[[Category: Metal-binding]]
-[[Category: Oxidoreductase]]
-[[Category: Respiratory chain]]
-[[Category: Transmembrane]]
-[[Category: Transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 22 11:32:28 2009''