4ysa: Difference between revisions

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-'''Unreleased structure'''
-The entry 4ysa is ON HOLD
+==Completely oxidized structure of copper nitrite reductase from Geobacillus thermodenitrificans==
+<StructureSection load='4ysa' size='340' side='right'caption='[[4ysa]], [[Resolution|resolution]] 1.43&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4ysa]] 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=4YSA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YSA 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]] 1.43&#8491;</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=NA:SODIUM+ION'>NA</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=4ysa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ysa OCA], [https://pdbe.org/4ysa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ysa RCSB], [https://www.ebi.ac.uk/pdbsum/4ysa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ysa ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A4IL26_GEOTN A4IL26_GEOTN]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-Authors: Fukuda, Y., Tse, K.M., 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.
+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>
-Description: Completely oxidized structure of copper nitrite reductase from Geobacillus thermodenitrificans
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Nureki, O]]
+<div class="pdbe-citations 4ysa" style="background-color:#fffaf0;"></div>
-[[Category: Tse, K.M]]
-[[Category: Inoue, T]]
+==See Also==
-[[Category: Diederichs, K]]
+*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
-[[Category: Suzuki, M]]
+== References ==
-[[Category: Iwata, S]]
+<references/>
-[[Category: Matsumura, H]]
+__TOC__
-[[Category: Sugahara, M]]
+</StructureSection>
-[[Category: Hirata, K]]
+[[Category: Geobacillus thermodenitrificans NG80-2]]
-[[Category: Mizohata, E]]
+[[Category: Large Structures]]
-[[Category: Nango, E]]
+[[Category: Diederichs K]]
-[[Category: Fukuda, Y]]
+[[Category: Fukuda Y]]
-[[Category: Song, C]]
+[[Category: Hatsui T]]
-[[Category: Hatsui, T]]
+[[Category: Hirata K]]
-[[Category: Tono, K]]
+[[Category: Inoue T]]
-[[Category: Nakane, T]]
+[[Category: Iwata S]]
-[[Category: Yabashi, M]]
+[[Category: Joti Y]]
-[[Category: Joti, Y]]
+[[Category: Kameshima T]]
-[[Category: Kameshima, T]]
+[[Category: Matsumura H]]
+[[Category: Mizohata E]]
+[[Category: Nakane T]]
+[[Category: Nango E]]
+[[Category: Nureki O]]
+[[Category: Song C]]
+[[Category: Sugahara M]]
+[[Category: Suzuki M]]
+[[Category: Tono K]]
+[[Category: Tse KM]]
+[[Category: Yabashi M]]