6kv0: Difference between revisions
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<StructureSection load='6kv0' size='340' side='right'caption='[[6kv0]], [[Resolution|resolution]] 1.40Å' scene=''> | <StructureSection load='6kv0' size='340' side='right'caption='[[6kv0]], [[Resolution|resolution]] 1.40Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'> | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KV0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KV0 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]] 1.4Å</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]] 1.4Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr> | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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=6kv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kv0 OCA], [https://pdbe.org/6kv0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kv0 RCSB], [https://www.ebi.ac.uk/pdbsum/6kv0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kv0 ProSAT]</span></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=6kv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kv0 OCA], [https://pdbe.org/6kv0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kv0 RCSB], [https://www.ebi.ac.uk/pdbsum/6kv0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kv0 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== | <div style="background-color:#fffaf0;"> | ||
[ | == Publication Abstract from PubMed == | ||
Plant-type ferredoxin (Fd) is an electron transfer protein in chloroplast. Redox-dependent structural change of Fd controls its association with and dissociation from Fd-dependent enzymes. Among many X-ray structures of oxidized Fd have been reported so far, very likely a given number of them was partially reduced by strong X-ray. To understand the precise structural change between reduced and oxidized Fd, it is important to know whether the crystals of oxidized Fd may or may not be reduced during the X-ray experiment. We prepared the thin plate-shaped Fd crystals from Chlamydomonas reinhardtii and monitored its absorption spectra during experiment. Absorption spectra of oxidized Fd crystals were clearly changed to that of reduced form in an X-ray dose-dependent manner. In another independent experiment, the X-ray diffraction images obtained from different parts of one single crystal were sorted and merged to form two datasets with low and high X-ray doses. An Fo-Fo map calculated from the two datasets showed that X-ray reduction causes a small displacement of the iron atoms in the [2Fe-2S] cluster. Both our spectroscopic and crystallographic studies confirm X-ray dose-dependent reduction of Fd, and suggest a structural basis for its initial reduction step especially in the core of the cluster. | |||
X-ray dose-dependent structural changes of the [2Fe-2S] ferredoxin from Chlamydomonas reinhardtii.,Ohnishi Y, Muraki N, Kiyota D, Okumura H, Baba S, Kawano Y, Kumasaka T, Tanaka H, Kurisu G J Biochem. 2020 Apr 13. pii: 5819557. doi: 10.1093/jb/mvaa045. PMID:32282907<ref>PMID:32282907</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6kv0" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Ferredoxin 3D structures|Ferredoxin 3D structures]] | *[[Ferredoxin 3D structures|Ferredoxin 3D structures]] | ||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Kurisu G]] | [[Category: Kurisu G]] | ||
[[Category: Onishi Y]] | [[Category: Onishi Y]] | ||
[[Category: Tanaka H]] | [[Category: Tanaka H]] | ||
Latest revision as of 13:24, 13 August 2026
Ferredoxin I from C. reinhardtii, high X-ray dose
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