5og5 - Revision history

OCA at 16:48, 13 December 2023

OCA — Wed, 13 Dec 2023 16:48:56 GMT

←Older revision		Revision as of 16:48, 13 December 2023
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	<StructureSection load='5og5' size='340' side='right'caption='[[5og5]], [[Resolution\|resolution]] 1.82Å' scene=''>		<StructureSection load='5og5' size='340' side='right'caption='[[5og5]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5og5]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OG5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5OG5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5og5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Achromobacter_cycloclastes Achromobacter cycloclastes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OG5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OG5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NO:NITRIC+OXIDE'>NO</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</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]] 1.82Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NO:NITRIC+OXIDE'>NO</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</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=5og5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5og5 OCA], [~~http~~://pdbe.org/5og5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5og5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5og5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5og5 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=5og5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5og5 OCA], [https://pdbe.org/5og5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5og5 RCSB], [https://www.ebi.ac.uk/pdbsum/5og5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5og5 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/NIR_ACHCY NIR_ACHCY]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Achromobacter cycloclastes]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Horrell, S]]	+	[[Category: Horrell S]]
-	[[Category: Hough~~, M A~~]]	+	[[Category: Hough MA]]
-	[[Category: Kekilli, D]]	+	[[Category: Kekilli D]]
-	[[Category: Strange~~, R W]]~~	+	[[Category: Strange RW]]
-	~~[[Category: Electron transfer]]~~	+
-	~~[[Category: Nitrite reductase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 12:23, 26 August 2020

OCA — Wed, 26 Aug 2020 12:23:01 GMT

←Older revision		Revision as of 12:23, 26 August 2020
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	==Cu nitrite reductase serial data at varying temperatures RT 0.21MGy==		==Cu nitrite reductase serial data at varying temperatures RT 0.21MGy==
-	<StructureSection load='5og5' size='340' side='right' caption='[[5og5]], [[Resolution\|resolution]] 1.82Å' scene=''>	+	<StructureSection load='5og5' size='340' side='right'caption='[[5og5]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5og5]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OG5 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OG5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5og5]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OG5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5OG5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NO:NITRIC+OXIDE'>NO</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NO:NITRIC+OXIDE'>NO</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5og5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5og5 OCA], [http://pdbe.org/5og5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5og5 RCSB], [http://www.ebi.ac.uk/pdbsum/5og5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5og5 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=5og5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5og5 OCA], [http://pdbe.org/5og5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5og5 RCSB], [http://www.ebi.ac.uk/pdbsum/5og5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5og5 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5og5" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5og5" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitrite reductase 3D structures\|Nitrite reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Horrell, S]]		[[Category: Horrell, S]]
	[[Category: Hough, M A]]		[[Category: Hough, M A]]

OCA at 07:13, 23 May 2018

OCA — Wed, 23 May 2018 07:13:23 GMT

←Older revision		Revision as of 07:13, 23 May 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5og5 is ~~ON HOLD until Paper~~ Publication	+	==Cu nitrite reductase serial data at varying temperatures RT 0.21MGy==
		+	<StructureSection load='5og5' size='340' side='right' caption='[[5og5]], [[Resolution\|resolution]] 1.82Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5og5]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OG5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OG5 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NO:NITRIC+OXIDE'>NO</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5og5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5og5 OCA], [http://pdbe.org/5og5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5og5 RCSB], [http://www.ebi.ac.uk/pdbsum/5og5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5og5 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	High-resolution crystal structures of enzymes in relevant redox states have transformed our understanding of enzyme catalysis. Recent developments have demonstrated that X-rays can be used, via the generation of solvated electrons, to drive reactions in crystals at cryogenic temperatures (100 K) to generate 'structural movies' of enzyme reactions. However, a serious limitation at these temperatures is that protein conformational motion can be significantly supressed. Here, the recently developed MSOX (multiple serial structures from one crystal) approach has been applied to nitrite-bound copper nitrite reductase at room temperature and at 190 K, close to the glass transition. During both series of multiple structures, nitrite was initially observed in a 'top-hat' geometry, which was rapidly transformed to a 'side-on' configuration before conversion to side-on NO, followed by dissociation of NO and substitution by water to reform the resting state. Density functional theory calculations indicate that the top-hat orientation corresponds to the oxidized type 2 copper site, while the side-on orientation is consistent with the reduced state. It is demonstrated that substrate-to-product conversion within the crystal occurs at a lower radiation dose at 190 K, allowing more of the enzyme catalytic cycle to be captured at high resolution than in the previous 100 K experiment. At room temperature the reaction was very rapid, but it remained possible to generate and characterize several structural states. These experiments open up the possibility of obtaining MSOX structural movies at multiple temperatures (MSOX-VT), providing an unparallelled level of structural information during catalysis for redox enzymes.

-	~~Authors: Horrell~~, S., Kekilli, D., Strange, R.W.~~, Hough, M~~.A.	+	Enzyme catalysis captured using multiple structures from one crystal at varying temperatures.,Horrell S, Kekilli D, Sen K, Owen RL, Dworkowski FSN, Antonyuk SV, Keal TW, Yong CW, Eady RR, Hasnain SS, Strange RW, Hough MA IUCrJ. 2018 Mar 16;5(Pt 3):283-292. doi: 10.1107/S205225251800386X. eCollection, 2018 May 1. PMID:29755744<ref>PMID:29755744</ref>

-	~~Description: Cu nitrite reductase serial data at varying temperatures RT 0~~.~~21MGy~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Kekilli, D]]~~	+	<div class="pdbe-citations 5og5" style="background-color:#fffaf0;"></div>
-	~~[[Category: Hough, M.A]]~~	+	== References ==
-	~~[[Category: Strange, R.W]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Horrell, S]]		[[Category: Horrell, S]]
		+	[[Category: Hough, M A]]
		+	[[Category: Kekilli, D]]
		+	[[Category: Strange, R W]]
		+	[[Category: Electron transfer]]
		+	[[Category: Nitrite reductase]]
		+	[[Category: Oxidoreductase]]

OCA at 04:46, 20 December 2017

OCA — Wed, 20 Dec 2017 04:46:47 GMT

←Older revision		Revision as of 04:46, 20 December 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5og5 is ON HOLD	+	The entry 5og5 is ON HOLD until Paper Publication

	Authors: Horrell, S., Kekilli, D., Strange, R.W., Hough, M.A.		Authors: Horrell, S., Kekilli, D., Strange, R.W., Hough, M.A.

-	Description: Cu nitrite reductase serial data at varying temperatures RT 0.~~35MGy~~	+	Description: Cu nitrite reductase serial data at varying temperatures RT 0.21MGy
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Kekilli, D]]		[[Category: Kekilli, D]]

OCA: Protected "5og5" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 12:23:33 GMT

Protected "5og5" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:23, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5og5 is ON HOLD Authors: Horrell, S., Kekilli, D., Strange, R.W., Hough, M.A. Description: Cu nitrite reductase serial data at varying temperatures...

OCA — Wed, 27 Sep 2017 12:23:32 GMT

New page: '''Unreleased structure''' The entry 5og5 is ON HOLD Authors: Horrell, S., Kekilli, D., Strange, R.W., Hough, M.A. Description: Cu nitrite reductase serial data at varying temperatures...

New page

'''Unreleased structure'''

The entry 5og5 is ON HOLD

Authors: Horrell, S., Kekilli, D., Strange, R.W., Hough, M.A.

Description: Cu nitrite reductase serial data at varying temperatures RT 0.35MGy
[[Category: Unreleased Structures]]
[[Category: Kekilli, D]]
[[Category: Hough, M.A]]
[[Category: Strange, R.W]]
[[Category: Horrell, S]]