1jfb: Difference between revisions

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OCA

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-[[Image:1jfb.jpg|left|200px]]<br /><applet load="1jfb" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1jfb, resolution 1.0&Aring;" />
-'''X-ray structure of nitric oxide reductase (cytochrome P450nor) in the ferric resting state at atomic resolution'''<br />
-==Overview==
+==X-ray structure of nitric oxide reductase (cytochrome P450nor) in the ferric resting state at atomic resolution==
-Crystal structures of the nitric oxide reductase cytochrome P450nor, (P450nor) in the ferric resting and the ferrous carbonmonoxy (CO) states, have been determined at 1.00 and 1.05 A resolution, respectively. P450nor, consists of 403 amino-acid residues (46 kDa) and is one of the largest, proteins refined to this resolution so far. The final models have, conventional R factors of 10.2% (ferric resting) and 11.7% (ferrous CO), with mean coordinate errors of 0.028 (ferric resting) and 0.030 A (ferrous, CO) as calculated from inversion of the full positional least-squares, matrix. Owing to the atomic resolution, novel features are found in the, refined structures. Firstly, two orientations of the haem are observed, both in the ferric resting and the ferrous CO states. Secondly, a, disordered water molecule bound to the haem iron is found in the ferric, resting state. In addition, the accurate structures at atomic resolution, enabled the examination of general stereochemical parameters that are, commonly used in refinement cycles of protein structures.
+<StructureSection load='1jfb' size='340' side='right'caption='[[1jfb]], [[Resolution|resolution]] 1.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1jfb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusarium_oxysporum Fusarium oxysporum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JFB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JFB FirstGlance]. <br>
+</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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=1jfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jfb OCA], [https://pdbe.org/1jfb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jfb RCSB], [https://www.ebi.ac.uk/pdbsum/1jfb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jfb ProSAT], [https://www.topsan.org/Proteins/RSGI/1jfb TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NOR_FUSOX NOR_FUSOX] Nitric oxide reductase which is involved in a dissimilatory reduction of nitrite. Acts as a nitric oxide reductase. Is able to reduce nitrate and nitrite to a gaseous form of N(2)O when oxygen supply is limited or discontinued. May function as a detoxification mechanism.<ref>PMID:2040619</ref> <ref>PMID:12105197</ref>
+== 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/jf/1jfb_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=1jfb ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-JFB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Fusarium_oxysporum Fusarium oxysporum] with HEM and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Nitric-oxide_reductase Nitric-oxide reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.99.7 1.7.99.7] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1JFB OCA].
+*[[Cytochrome P450 3D structures|Cytochrome P450 3D structures]]
+== References ==
-==Reference==
+<references/>
-X-ray structure of nitric oxide reductase (cytochrome P450nor) at atomic resolution., Shimizu H, Park SY, Shiro Y, Adachi S, Acta Crystallogr D Biol Crystallogr. 2002 Jan;58(Pt 1):81-9. Epub 2001 Dec, 21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11752781 11752781]
+__TOC__
+</StructureSection>
 [[Category: Fusarium oxysporum]]
-[[Category: Nitric-oxide reductase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Adachi S]]
-[[Category: Adachi, S.]]
+[[Category: Park SY]]
-[[Category: Park, S.Y.]]
+[[Category: Shimizu H]]
-[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
+[[Category: Shiro Y]]
-[[Category: Shimizu, H.]]
-[[Category: Shiro, Y.]]
-[[Category: GOL]]
-[[Category: HEM]]
-[[Category: atomic resolution]]
-[[Category: cytochrome p450nor]]
-[[Category: nitric oxide reductase]]
-[[Category: riken structural genomics/proteomics initiative]]
-[[Category: rsgi]]
-[[Category: structural genomics]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:11:25 2007''