3ubr: Difference between revisions

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-[[Image:3ubr.png|left|200px]]
-<!--
+==Laue structure of Shewanella oneidensis cytochrome-c Nitrite Reductase==
-The line below this paragraph, containing "STRUCTURE_3ubr", creates the "Structure Box" on the page.
+<StructureSection load='3ubr' size='340' side='right'caption='[[3ubr]], [[Resolution|resolution]] 2.59&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'>[[3ubr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UBR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UBR 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]] 2.59&#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=HEC:HEME+C'>HEC</scene></td></tr>
-{{STRUCTURE_3ubr|  PDB=3ubr  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ubr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ubr OCA], [https://pdbe.org/3ubr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ubr RCSB], [https://www.ebi.ac.uk/pdbsum/3ubr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ubr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NRFA_SHEON NRFA_SHEON] Plays a role in nitrite reduction.[HAMAP-Rule:MF_01182]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The high-yield expression and purification of Shewanella oneidensis cytochrome c nitrite reductase (ccNiR) and its characterization by a variety of methods, notably Laue crystallography, are reported. A key component of the expression system is an artificial ccNiR gene in which the N-terminal signal peptide from the highly expressed S. oneidensis protein "small tetraheme c" replaces the wild-type signal peptide. This gene, inserted into the plasmid pHSG298 and expressed in S. oneidensis TSP-1 strain, generated approximately 20 mg crude ccNiR per liter of culture, compared with 0.5-1 mg/L for untransformed cells. Purified ccNiR has nitrite and hydroxylamine reductase activities comparable to those previously reported for Escherichia coli ccNiR, and is stable for over 2 weeks in pH 7 solution at 4 degrees C. UV/vis spectropotentiometric titrations and protein film voltammetry identified five independent one-electron reduction processes. Global analysis of the spectropotentiometric data also allowed determination of the extinction coefficient spectra for the five reduced ccNiR species. The characteristics of the individual extinction coefficient spectra suggest that, within each reduced species, the electrons are distributed among the various hemes, rather than being localized on specific heme centers. The purified ccNiR yielded good-quality crystals, with which the 2.59-A-resolution structure was solved at room temperature using the Laue diffraction method. The structure is similar to that of E. coli ccNiR, except in the region where the enzyme interacts with its physiological electron donor (CymA in the case of S. oneidensis ccNiR, NrfB in the case of the E. coli protein).
-===Laue structure of Shewanella oneidensis cytochrome-c Nitrite Reductase===
+Laue crystal structure of Shewanella oneidensis cytochrome c nitrite reductase from a high-yield expression system.,Youngblut M, Judd ET, Srajer V, Sayyed B, Goelzer T, Elliott SJ, Schmidt M, Pacheco AA J Biol Inorg Chem. 2012 Mar 2. PMID:22382353<ref>PMID:22382353</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_22382353}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3ubr" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 22382353 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_22382353}}
-==About this Structure==
-[[3ubr]] is a 2 chain structure of [[Nitric reductase]] with sequence from [http://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UBR OCA].
 ==See Also==
-*[[Journal:JBIC:16|Journal:JBIC:16]]
+*[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]]
-*[[Nitric reductase|Nitric reductase]]
+*[[Hemeproteins|Hemeproteins]]
+*[[Nitrite reductase|Nitrite reductase]]
-==Reference==
+== References ==
-<ref group="xtra">PMID:022382353</ref><references group="xtra"/>
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Shewanella oneidensis]]
-[[Category: Elliott, S.]]
+[[Category: Elliott S]]
-[[Category: Goeltzner, T.]]
+[[Category: Goeltzner T]]
-[[Category: Judd, E T.]]
+[[Category: Judd ET]]
-[[Category: Pacheco, A.]]
+[[Category: Pacheco A]]
-[[Category: Sayed, B.]]
+[[Category: Sayed B]]
-[[Category: Schmidt, M.]]
+[[Category: Schmidt M]]
-[[Category: Srajer, V.]]
+[[Category: Srajer V]]
-[[Category: Youngblut, M.]]
+[[Category: Youngblut M]]
-[[Category: Cyma]]
-[[Category: Deca-heme]]
-[[Category: Electron transfer]]
-[[Category: Oxidoreductase]]
-[[Category: Redox]]