4ysr: Difference between revisions

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 <StructureSection load='4ysr' size='340' side='right'caption='[[4ysr]], [[Resolution|resolution]] 1.34&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ysr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Geotn Geotn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YSR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YSR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ysr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans_NG80-2 Geobacillus thermodenitrificans NG80-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YSR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YSR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.34&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ysa|4ysa]], [[4ysc|4ysc]], [[4ysd|4ysd]], [[4yse|4yse]], [[4yso|4yso]], [[4ysp|4ysp]], [[4ysq|4ysq]], [[4yss|4yss]], [[4yst|4yst]], [[4ysu|4ysu]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nirK, GTNG_0650 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=420246 GEOTN])</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=4ysr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ysr OCA], [https://pdbe.org/4ysr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ysr RCSB], [https://www.ebi.ac.uk/pdbsum/4ysr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ysr ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ysr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ysr OCA], [http://pdbe.org/4ysr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ysr RCSB], [http://www.ebi.ac.uk/pdbsum/4ysr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ysr ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/A4IL26_GEOTN A4IL26_GEOTN]
-Serial femtosecond crystallography (SFX) has enabled the damage-free structural determination of metalloenzymes and filled the gaps of our knowledge between crystallographic and spectroscopic data. Crystallographers, however, scarcely know whether the rising technique provides truly new structural insights into mechanisms of metalloenzymes partly because of limited resolutions. Copper nitrite reductase (CuNiR), which converts nitrite to nitric oxide in denitrification, has been extensively studied by synchrotron radiation crystallography (SRX). Although catalytic Cu (Type 2 copper (T2Cu)) of CuNiR had been suspected to tolerate X-ray photoreduction, we here showed that T2Cu in the form free of nitrite is reduced and changes its coordination structure in SRX. Moreover, we determined the completely oxidized CuNiR structure at 1.43 A resolution with SFX. Comparison between the high-resolution SFX and SRX data revealed the subtle structural change of a catalytic His residue by X-ray photoreduction. This finding, which SRX has failed to uncover, provides new insight into the reaction mechanism of CuNiR.
-Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography.,Fukuda Y, Tse KM, Suzuki M, Diederichs K, Hirata K, Nakane T, Sugahara M, Nango E, Tono K, Joti Y, Kameshima T, Song C, Hatsui T, Yabashi M, Nureki O, Matsumura H, Inoue T, Iwata S, Mizohata E J Biochem. 2016 Jan 14. pii: mvv133. PMID:26769972<ref>PMID:26769972</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4ysr" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Nitrite reductase|Nitrite reductase]]
+*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Geotn]]
+[[Category: Geobacillus thermodenitrificans NG80-2]]
 [[Category: Large Structures]]
-[[Category: Diederichs, K]]
+[[Category: Diederichs K]]
-[[Category: Fukuda, Y]]
+[[Category: Fukuda Y]]
-[[Category: Hatsui, T]]
+[[Category: Hatsui T]]
-[[Category: Hirata, K]]
+[[Category: Hirata K]]
-[[Category: Inoue, T]]
+[[Category: Inoue T]]
-[[Category: Iwata, S]]
+[[Category: Iwata S]]
-[[Category: Joti, Y]]
+[[Category: Joti Y]]
-[[Category: Kameshima, T]]
+[[Category: Kameshima T]]
-[[Category: Matsumura, H]]
+[[Category: Matsumura H]]
-[[Category: Mizohata, E]]
+[[Category: Mizohata E]]
-[[Category: Nakane, T]]
+[[Category: Nakane T]]
-[[Category: Nango, E]]
+[[Category: Nango E]]
-[[Category: Nureki, O]]
+[[Category: Nureki O]]
-[[Category: Song, C]]
+[[Category: Song C]]
-[[Category: Sugahara, M]]
+[[Category: Sugahara M]]
-[[Category: Suzuki, M]]
+[[Category: Suzuki M]]
-[[Category: Tono, K]]
+[[Category: Tono K]]
-[[Category: Tse, K M]]
+[[Category: Tse KM]]
-[[Category: Yabashi, M]]
+[[Category: Yabashi M]]
-[[Category: Copper]]
-[[Category: Nitrite]]
-[[Category: Oxidoreductase]]
-[[Category: Reductase]]