6z7r - Revision history

OCA at 13:43, 24 January 2024

OCA — Wed, 24 Jan 2024 13:43:12 GMT

←Older revision		Revision as of 13:43, 24 January 2024
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-	====	+	==Structure of [NiFeSe] hydrogenase from Desulfovibrio vulgaris hildenborough pressurized with Krypton gas - structure wtKr1==
-	<StructureSection load='6z7r' size='340' side='right'caption='[[6z7r]]' scene=''>	+	<StructureSection load='6z7r' size='340' side='right'caption='[[6z7r]], [[Resolution\|resolution]] 1.77Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6z7r]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._Hildenborough Desulfovibrio vulgaris str. Hildenborough]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z7R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Z7R 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=6z7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z7r OCA], [~~http~~://pdbe.org/6z7r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6z7r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6z7r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6z7r ProSAT]</span></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]] 1.77Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6ML:OXYGEN-DAMAGED+SF4'>6ML</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=KR:KRYPTON'>KR</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=6z7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z7r OCA], [https://pdbe.org/6z7r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6z7r RCSB], [https://www.ebi.ac.uk/pdbsum/6z7r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6z7r ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q72AS4_DESVH Q72AS4_DESVH]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Hydrogenases are metalloenzymes that catalyse both H2 evolution and uptake. They are gas-processing enzymes with deeply buried active sites, so the gases diffuse through channels that connect the active site to the protein surface. The [NiFeSe] hydrogenases are a special class of hydrogenases containing a selenocysteine as a nickel ligand; they are more catalytically active and less O2-sensitive than standard [NiFe] hydrogenases. Characterisation of the channel system of hydrogenases is important to understand how the inhibitor oxygen reaches the active site to cause oxidative damage. To this end, crystals of Desulfovibrio vulgaris Hildenborough [NiFeSe] hydrogenase were pressurized with krypton and oxygen, and a method for tracking labile O2 molecules was developed, for mapping a hydrophobic channel system similar to that of the [NiFe] enzymes as the major route for gas diffusion.
		+
		+	Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen.,Zacarias S, Temporao A, Carpentier P, van der Linden P, Pereira IAC, Matias PM J Biol Inorg Chem. 2020 Aug 31. pii: 10.1007/s00775-020-01814-y. doi:, 10.1007/s00775-020-01814-y. PMID:32865640<ref>PMID:32865640</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6z7r" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Desulfovibrio vulgaris str. Hildenborough]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Carpentier P]]
		+	[[Category: Matias PM]]
		+	[[Category: Pereira IAC]]
		+	[[Category: Temporao A]]
		+	[[Category: Zacarias S]]
		+	[[Category: Van der Linden P]]

OCA at 09:35, 9 September 2020

OCA — Wed, 09 Sep 2020 09:35:54 GMT

←Older revision		Revision as of 09:35, 9 September 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6z7r ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='6z7r' size='340' side='right'caption='[[6z7r]]' scene=''>
-	~~Authors~~: ~~Zacarias, S~~.~~, Temporao, A~~.~~, Carpentier, P~~.~~, van der Linden, P~~.~~, Pereira, I~~.A.~~C., Matias, P.M~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Structure of~~ [~~NiFeSe] hydrogenase from Desulfovibrio vulgaris hildenborough pressurized with Krypton gas -structure wtKr1~~	+	</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=6z7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z7r OCA], [http://pdbe.org/6z7r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6z7r RCSB], [http://www.ebi.ac.uk/pdbsum/6z7r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6z7r ProSAT]</span></td></tr>
-	~~[[Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Pereira, I~~.A.C]]	+	__TOC__
-	[~~[Category~~: ~~Temporao, A]~~]	+	</StructureSection>
-	[[~~Category~~: ~~Zacarias, S~~]]	+	[[Category: Large Structures]]
-	[~~[Category~~: ~~Van Der Linden~~, P]]	+	[[Category: Z-disk]]
-	[[Category: ~~Matias, P.M~~]]	+
-	[[Category: ~~Carpentier, P~~]]	+

OCA at 18:35, 24 June 2020

OCA — Wed, 24 Jun 2020 18:35:25 GMT

←Older revision		Revision as of 18:35, 24 June 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6z7r is ON HOLD	+	The entry 6z7r is ON HOLD until Paper Publication

	Authors: Zacarias, S., Temporao, A., Carpentier, P., van der Linden, P., Pereira, I.A.C., Matias, P.M.		Authors: Zacarias, S., Temporao, A., Carpentier, P., van der Linden, P., Pereira, I.A.C., Matias, P.M.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Pereira, I.A.C]]		[[Category: Pereira, I.A.C]]
-	[[Category: Van Der Linden, P]]
	[[Category: Temporao, A]]		[[Category: Temporao, A]]
		+	[[Category: Zacarias, S]]
		+	[[Category: Van Der Linden, P]]
	[[Category: Matias, P.M]]		[[Category: Matias, P.M]]
	[[Category: Carpentier, P]]		[[Category: Carpentier, P]]
-	[[Category: Zacarias, S]]

OCA: Protected "6z7r" [edit=sysop:move=sysop]

OCA — Wed, 10 Jun 2020 05:08:42 GMT

Protected "6z7r" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:08, 10 June 2020

OCA: New page: '''Unreleased structure''' The entry 6z7r is ON HOLD Authors: Zacarias, S., Temporao, A., Carpentier, P., van der Linden, P., Pereira, I.A.C., Matias, P.M. Description: Structure of [N...

OCA — Wed, 10 Jun 2020 05:08:41 GMT

New page: '''Unreleased structure''' The entry 6z7r is ON HOLD Authors: Zacarias, S., Temporao, A., Carpentier, P., van der Linden, P., Pereira, I.A.C., Matias, P.M. Description: Structure of [N...

New page

'''Unreleased structure'''

The entry 6z7r is ON HOLD

Authors: Zacarias, S., Temporao, A., Carpentier, P., van der Linden, P., Pereira, I.A.C., Matias, P.M.

Description: Structure of [NiFeSe] hydrogenase from Desulfovibrio vulgaris hildenborough pressurized with Krypton gas -structure wtKr1
[[Category: Unreleased Structures]]
[[Category: Pereira, I.A.C]]
[[Category: Van Der Linden, P]]
[[Category: Temporao, A]]
[[Category: Matias, P.M]]
[[Category: Carpentier, P]]
[[Category: Zacarias, S]]