6tg9 - Revision history

OCA at 10:18, 22 May 2024

OCA — Wed, 22 May 2024 10:18:07 GMT

←Older revision		Revision as of 10:18, 22 May 2024
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	<StructureSection load='6tg9' size='340' side='right'caption='[[6tg9]], [[Resolution\|resolution]] 3.24Å' scene=''>		<StructureSection load='6tg9' size='340' side='right'caption='[[6tg9]], [[Resolution\|resolution]] 3.24Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6tg9]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Rhodobacter_capsulatus_y262~~ Rhodobacter capsulatus ~~y262~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TG9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6TG9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tg9]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacter_capsulatus_Y262 Rhodobacter capsulatus Y262]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TG9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6MO:MOLYBDENUM(VI)+ION'>6MO</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=MGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>MGD</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.24Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">U715_16550 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1415161 Rhodobacter capsulatus Y262]), U715_16555 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1415161 Rhodobacter capsulatus Y262]), U715_16560 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1415161 Rhodobacter capsulatus Y262]), U715_16540 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1415161 Rhodobacter capsulatus Y262])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6MO:MOLYBDENUM(VI)+ION'>6MO</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=MGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>MGD</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formate_dehydrogenase Formate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.2 1.2.1.2] </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=6tg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tg9 OCA], [https://pdbe.org/6tg9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tg9 RCSB], [https://www.ebi.ac.uk/pdbsum/6tg9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tg9 ProSAT]</span></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=6tg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tg9 OCA], [~~http~~://pdbe.org/6tg9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6tg9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6tg9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6tg9 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D5AQH0_RHOCB D5AQH0_RHOCB]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6tg9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6tg9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Formate dehydrogenase 3D structures\|Formate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Formate dehydrogenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Rhodobacter capsulatus ~~y262~~]]	+	[[Category: Rhodobacter capsulatus Y262]]
-	[[Category: Mittelstaedt, G]]	+	[[Category: Mittelstaedt G]]
-	[[Category: Radon, C]]	+	[[Category: Radon C]]
-	[[Category: Wendler, P]]	+	[[Category: Wendler P]]
-	~~[[Category: Formate oxidation]]~~	+
-	~~[[Category: Molybdoenzyme]]~~	+
-	~~[[Category: Nad+-dependent]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:08, 29 April 2020

OCA — Wed, 29 Apr 2020 07:08:28 GMT

←Older revision		Revision as of 07:08, 29 April 2020
Line 1:		Line 1:

	==Cryo-EM Structure of NADH reduced form of NAD+-dependent Formate Dehydrogenase from Rhodobacter capsulatus==		==Cryo-EM Structure of NADH reduced form of NAD+-dependent Formate Dehydrogenase from Rhodobacter capsulatus==
-	<StructureSection load='6tg9' size='340' side='right'caption='[[6tg9]]' scene=''>	+	<StructureSection load='6tg9' size='340' side='right'caption='[[6tg9]], [[Resolution\|resolution]] 3.24Å' 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=6TG9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TG9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tg9]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_capsulatus_y262 Rhodobacter capsulatus y262]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TG9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TG9 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=6tg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tg9 OCA], [http://pdbe.org/6tg9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tg9 RCSB], [http://www.ebi.ac.uk/pdbsum/6tg9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tg9 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=6MO:MOLYBDENUM(VI)+ION'>6MO</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=MGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>MGD</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">U715_16550 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1415161 Rhodobacter capsulatus Y262]), U715_16555 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1415161 Rhodobacter capsulatus Y262]), U715_16560 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1415161 Rhodobacter capsulatus Y262]), U715_16540 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1415161 Rhodobacter capsulatus Y262])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formate_dehydrogenase Formate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.2 1.2.1.2] </span></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=6tg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tg9 OCA], [http://pdbe.org/6tg9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tg9 RCSB], [http://www.ebi.ac.uk/pdbsum/6tg9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tg9 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Metal-containing formate dehydrogenases (FDH) catalyse the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active site. They display a diverse subunit and cofactor composition, but structural information on these enzymes is limited. Here we report the cryo-electron microscopic structures of the soluble Rhodobacter capsulatus FDH (RcFDH) as isolated and in the presence of reduced nicotinamide adenine dinucleotide (NADH). RcFDH assembles into a 360 kDa dimer of heterotetramers revealing a putative interconnection of electron pathway chains. In the presence of NADH, the RcFDH structure shows charging of cofactors, indicative of an increased electron load.
		+
		+	Cryo-EM structures reveal intricate Fe-S cluster arrangement and charging in Rhodobacter capsulatus formate dehydrogenase.,Radon C, Mittelstadt G, Duffus BR, Burger J, Hartmann T, Mielke T, Teutloff C, Leimkuhler S, Wendler P Nat Commun. 2020 Apr 20;11(1):1912. doi: 10.1038/s41467-020-15614-0. PMID:32313256<ref>PMID:32313256</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6tg9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Formate dehydrogenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Mittelstaedt G]]	+	[[Category: Rhodobacter capsulatus y262]]
-	[[Category: Radon C]]	+	[[Category: Mittelstaedt, G]]
-	[[Category: Wendler P]]	+	[[Category: Radon, C]]
		+	[[Category: Wendler, P]]
		+	[[Category: Formate oxidation]]
		+	[[Category: Molybdoenzyme]]
		+	[[Category: Nad+-dependent]]
		+	[[Category: Oxidoreductase]]

OCA at 05:44, 22 April 2020

OCA — Wed, 22 Apr 2020 05:44:33 GMT

←Older revision		Revision as of 05:44, 22 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6tg9 is ~~ON HOLD~~	+	==Cryo-EM Structure of NADH reduced form of NAD+-dependent Formate Dehydrogenase from Rhodobacter capsulatus==
-		+	<StructureSection load='6tg9' size='340' side='right'caption='[[6tg9]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TG9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TG9 FirstGlance]. <br>
-	~~Description~~:	+	</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=6tg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tg9 OCA], [http://pdbe.org/6tg9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tg9 RCSB], [http://www.ebi.ac.uk/pdbsum/6tg9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tg9 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Mittelstaedt G]]
		+	[[Category: Radon C]]
		+	[[Category: Wendler P]]

OCA: Protected "6tg9" [edit=sysop:move=sysop]

OCA — Wed, 27 Nov 2019 05:13:58 GMT

Protected "6tg9" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:13, 27 November 2019

OCA: New page: '''Unreleased structure''' The entry 6tg9 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Nov 2019 05:13:57 GMT

New page: '''Unreleased structure''' The entry 6tg9 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6tg9 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]