6lk1 - Revision history

OCA at 11:02, 22 November 2023

OCA — Wed, 22 Nov 2023 11:02:39 GMT

←Older revision		Revision as of 11:02, 22 November 2023
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	<StructureSection load='6lk1' size='340' side='right'caption='[[6lk1]], [[Resolution\|resolution]] 0.90Å' scene=''>		<StructureSection load='6lk1' size='340' side='right'caption='[[6lk1]], [[Resolution\|resolution]] 0.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6lk1]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Chlre Chlre~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LK1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6LK1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lk1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii Chlamydomonas reinhardtii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LK1 FirstGlance]. <br>
-	</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=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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]] 0.9Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PETF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3055 CHLRE])~~</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=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6lk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lk1 OCA], [~~http~~://pdbe.org/6lk1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6lk1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6lk1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6lk1 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=6lk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lk1 OCA], [https://pdbe.org/6lk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lk1 RCSB], [https://www.ebi.ac.uk/pdbsum/6lk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lk1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/FER_CHLRE FER_CHLRE]] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.	+	[https://www.uniprot.org/uniprot/FER_CHLRE FER_CHLRE] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6lk1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6lk1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ferredoxin 3D structures\|Ferredoxin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Chlre~~]]	+	[[Category: Chlamydomonas reinhardtii]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kurisu, G]]	+	[[Category: Kurisu G]]
-	[[Category: Onishi, Y]]	+	[[Category: Onishi Y]]
-	[[Category: Tanaka, H]]	+	[[Category: Tanaka H]]
-	~~[[Category: Electron transport~~]]	+

OCA at 06:35, 10 June 2020

OCA — Wed, 10 Jun 2020 06:35:47 GMT

←Older revision		Revision as of 06:35, 10 June 2020
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	==Ultrahigh resolution X-ray structure of Ferredoxin I from C. reinhardtii==		==Ultrahigh resolution X-ray structure of Ferredoxin I from C. reinhardtii==
-	<StructureSection load='6lk1' size='340' side='right'caption='[[6lk1]]' scene=''>	+	<StructureSection load='6lk1' size='340' side='right'caption='[[6lk1]], [[Resolution\|resolution]] 0.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LK1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LK1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lk1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Chlre Chlre]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LK1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LK1 FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6lk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lk1 OCA], [http://pdbe.org/6lk1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lk1 RCSB], [http://www.ebi.ac.uk/pdbsum/6lk1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lk1 ProSAT]</span></td></tr>	+	</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=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</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">PETF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3055 CHLRE])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6lk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lk1 OCA], [http://pdbe.org/6lk1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lk1 RCSB], [http://www.ebi.ac.uk/pdbsum/6lk1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lk1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FER_CHLRE FER_CHLRE]] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.
		+	<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 6lk1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Chlre]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kurisu G]]	+	[[Category: Kurisu, G]]
-	[[Category: Onishi Y]]	+	[[Category: Onishi, Y]]
-	[[Category: Tanaka H]]	+	[[Category: Tanaka, H]]
		+	[[Category: Electron transport]]

OCA at 06:53, 27 May 2020

OCA — Wed, 27 May 2020 06:53:29 GMT

←Older revision		Revision as of 06:53, 27 May 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6lk1 ~~is ON HOLD until Paper Publication~~	+	==Ultrahigh resolution X-ray structure of Ferredoxin I from C. reinhardtii==
-		+	<StructureSection load='6lk1' size='340' side='right'caption='[[6lk1]]' scene=''>
-	~~Authors~~: ~~Onishi~~, Y.~~, Kurisu, G~~., ~~Tanaka~~, H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LK1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LK1 FirstGlance]. <br>
-	~~Description~~: ~~Ferredoxin I from C~~. ~~reinhardtii~~, ~~low X~~-~~ray dose~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6lk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lk1 OCA], [http://pdbe.org/6lk1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lk1 RCSB], [http://www.ebi.ac.uk/pdbsum/6lk1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lk1 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Onishi, Y~~]]	+	__TOC__
-	[[Category: ~~Tanaka, H~~]]	+	</StructureSection>
-	[[Category: ~~Kurisu, G~~]]	+	[[Category: Large Structures]]
		+	[[Category: Kurisu G]]
		+	[[Category: Onishi Y]]
		+	[[Category: Tanaka H]]

OCA at 04:08, 20 May 2020

OCA — Wed, 20 May 2020 04:08:24 GMT

←Older revision		Revision as of 04:08, 20 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6lk1 is ON HOLD	+	The entry 6lk1 is ON HOLD until Paper Publication

	Authors: Onishi, Y., Kurisu, G., Tanaka, H.		Authors: Onishi, Y., Kurisu, G., Tanaka, H.
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	Description: Ferredoxin I from C. reinhardtii, low X-ray dose		Description: Ferredoxin I from C. reinhardtii, low X-ray dose
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Onishi, Y]]
	[[Category: Tanaka, H]]		[[Category: Tanaka, H]]
	[[Category: Kurisu, G]]		[[Category: Kurisu, G]]
-	[[Category: Onishi, Y]]

OCA: Protected "6lk1" [edit=sysop:move=sysop]

OCA — Wed, 25 Dec 2019 07:09:04 GMT

Protected "6lk1" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:09, 25 December 2019

OCA: New page: '''Unreleased structure''' The entry 6lk1 is ON HOLD Authors: Onishi, Y., Kurisu, G., Tanaka, H. Description: Ferredoxin I from C. reinhardtii, low X-ray dose [[Category: Unreleased St...

OCA — Wed, 25 Dec 2019 07:09:02 GMT

New page: '''Unreleased structure''' The entry 6lk1 is ON HOLD Authors: Onishi, Y., Kurisu, G., Tanaka, H. Description: Ferredoxin I from C. reinhardtii, low X-ray dose [[Category: Unreleased St...

New page

'''Unreleased structure'''

The entry 6lk1 is ON HOLD

Authors: Onishi, Y., Kurisu, G., Tanaka, H.

Description: Ferredoxin I from C. reinhardtii, low X-ray dose
[[Category: Unreleased Structures]]
[[Category: Tanaka, H]]
[[Category: Kurisu, G]]
[[Category: Onishi, Y]]