2vm4 - Revision history

OCA at 15:24, 13 December 2023

2023-12-13T15:24:51Z

← Older revision		Revision as of 15:24, 13 December 2023
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	<StructureSection load='2vm4' size='340' side='right'caption='[[2vm4]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2vm4' size='340' side='right'caption='[[2vm4]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2vm4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"achromobacter_xylosoxidans"_yabuuchi_and_ohyama_1971 "achromobacter~~ xylosoxidans~~" yabuuchi and ohyama 1971~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VM4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2vm4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Achromobacter_xylosoxidans Achromobacter xylosoxidans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VM4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.9Å</td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1bq5\|1bq5]], [[1gs6\|1gs6]], [[1gs8\|1gs8]], [[1hau\|1hau]], [[1haw\|1haw]], [[1ndt\|1ndt]], [[1oe3\|1oe3]], [[1wa0\|1wa0]], [[1wa2\|1wa2]], [[2jfc\|2jfc]], [[1gs7\|1gs7]], [[1oe1\|1oe1]], [[1oe2\|1oe2]], [[1wa1\|1wa1]], [[1wae\|1wae]], [[2bo0\|2bo0]], [[2bp0\|2bp0]], [[2bp8\|2bp8]], [[2vm3\|2vm3]]</div></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2vm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vm4 OCA], [https://pdbe.org/2vm4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vm4 RCSB], [https://www.ebi.ac.uk/pdbsum/2vm4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vm4 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=2vm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vm4 OCA], [https://pdbe.org/2vm4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vm4 RCSB], [https://www.ebi.ac.uk/pdbsum/2vm4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vm4 ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/O68601_ALCXX O68601_ALCXX]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Achromobacter xylosoxidans ~~yabuuchi and ohyama 1971~~]]		[[Category: Achromobacter xylosoxidans]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Antonyuk~~, S V~~]]		[[Category: Antonyuk SV]]
	[[Category: Eady~~, R R~~]]		[[Category: Eady RR]]
	[[Category: Hasnain~~, S S~~]]		[[Category: Hasnain SS]]
	[[Category: Hough~~, M A~~]]		[[Category: Hough MA]]
	[[Category: Strange~~, R W]]~~		[[Category: Strange RW]]
	~~[[Category: Denitrification]]~~
	~~[[Category: Nitrite reductase]]~~
	~~[[Category: Ordered mechanism]]~~
	~~[[Category: Oxidoreductase~~]]

OCA at 11:40, 30 March 2022

2022-03-30T11:40:06Z

← Older revision		Revision as of 11:40, 30 March 2022
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	<StructureSection load='2vm4' size='340' side='right'caption='[[2vm4]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2vm4' size='340' side='right'caption='[[2vm4]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2vm4]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"achromobacter_xylosoxidans"_yabuuchi_and_ohyama_1971 "achromobacter xylosoxidans" yabuuchi and ohyama 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VM4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2VM4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2vm4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"achromobacter_xylosoxidans"_yabuuchi_and_ohyama_1971 "achromobacter xylosoxidans" yabuuchi and ohyama 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VM4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bq5\|1bq5]], [[1gs6\|1gs6]], [[1gs8\|1gs8]], [[1hau\|1hau]], [[1haw\|1haw]], [[1ndt\|1ndt]], [[1oe3\|1oe3]], [[1wa0\|1wa0]], [[1wa2\|1wa2]], [[2jfc\|2jfc]], [[1gs7\|1gs7]], [[1oe1\|1oe1]], [[1oe2\|1oe2]], [[1wa1\|1wa1]], [[1wae\|1wae]], [[2bo0\|2bo0]], [[2bp0\|2bp0]], [[2bp8\|2bp8]], [[2vm3\|2vm3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1bq5\|1bq5]], [[1gs6\|1gs6]], [[1gs8\|1gs8]], [[1hau\|1hau]], [[1haw\|1haw]], [[1ndt\|1ndt]], [[1oe3\|1oe3]], [[1wa0\|1wa0]], [[1wa2\|1wa2]], [[2jfc\|2jfc]], [[1gs7\|1gs7]], [[1oe1\|1oe1]], [[1oe2\|1oe2]], [[1wa1\|1wa1]], [[1wae\|1wae]], [[2bo0\|2bo0]], [[2bp0\|2bp0]], [[2bp8\|2bp8]], [[2vm3\|2vm3]]</div></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=2vm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vm4 OCA], [~~http~~://pdbe.org/2vm4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2vm4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2vm4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2vm4 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=2vm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vm4 OCA], [https://pdbe.org/2vm4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vm4 RCSB], [https://www.ebi.ac.uk/pdbsum/2vm4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vm4 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 08:07, 25 June 2020

2020-06-25T08:07:46Z

← Older revision		Revision as of 08:07, 25 June 2020
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	==Structure of Alcaligenes xylosoxidans nitrite reductase in space group R3 - 2 of 2==		==Structure of Alcaligenes xylosoxidans nitrite reductase in space group R3 - 2 of 2==
	<StructureSection load='2vm4' size='340' side='right' caption='[[2vm4]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2vm4' size='340' side='right'caption='[[2vm4]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2vm4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_xylosoxidans"_yabuuchi_and_ohyama_1971 "achromobacter xylosoxidans" yabuuchi and ohyama 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VM4 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2VM4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2vm4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_xylosoxidans"_yabuuchi_and_ohyama_1971 "achromobacter xylosoxidans" yabuuchi and ohyama 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VM4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2VM4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bq5\|1bq5]], [[1gs6\|1gs6]], [[1gs8\|1gs8]], [[1hau\|1hau]], [[1haw\|1haw]], [[1ndt\|1ndt]], [[1oe3\|1oe3]], [[1wa0\|1wa0]], [[1wa2\|1wa2]], [[2jfc\|2jfc]], [[1gs7\|1gs7]], [[1oe1\|1oe1]], [[1oe2\|1oe2]], [[1wa1\|1wa1]], [[1wae\|1wae]], [[2bo0\|2bo0]], [[2bp0\|2bp0]], [[2bp8\|2bp8]], [[2vm3\|2vm3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bq5\|1bq5]], [[1gs6\|1gs6]], [[1gs8\|1gs8]], [[1hau\|1hau]], [[1haw\|1haw]], [[1ndt\|1ndt]], [[1oe3\|1oe3]], [[1wa0\|1wa0]], [[1wa2\|1wa2]], [[2jfc\|2jfc]], [[1gs7\|1gs7]], [[1oe1\|1oe1]], [[1oe2\|1oe2]], [[1wa1\|1wa1]], [[1wae\|1wae]], [[2bo0\|2bo0]], [[2bp0\|2bp0]], [[2bp8\|2bp8]], [[2vm3\|2vm3]]</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=2vm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vm4 OCA], [http://pdbe.org/2vm4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vm4 RCSB], [http://www.ebi.ac.uk/pdbsum/2vm4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vm4 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=2vm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vm4 OCA], [http://pdbe.org/2vm4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vm4 RCSB], [http://www.ebi.ac.uk/pdbsum/2vm4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vm4 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	==See Also==		==See Also==
	*[[Nitrite reductase\|Nitrite reductase]]		*[[Nitrite reductase 3D structures\|Nitrite reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Achromobacter xylosoxidans yabuuchi and ohyama 1971]]		[[Category: Achromobacter xylosoxidans yabuuchi and ohyama 1971]]
			[[Category: Large Structures]]
	[[Category: Antonyuk, S V]]		[[Category: Antonyuk, S V]]
	[[Category: Eady, R R]]		[[Category: Eady, R R]]

OCA at 20:56, 19 September 2018

2018-09-19T20:56:45Z

← Older revision		Revision as of 20:56, 19 September 2018
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	==~~STRUCTURE OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE IN SPACE GROUP~~ R3 - 2 OF 2==
			==Structure of Alcaligenes xylosoxidans nitrite reductase in space group R3 - 2 of 2==
	<StructureSection load='2vm4' size='340' side='right' caption='[[2vm4]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2vm4' size='340' side='right' caption='[[2vm4]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bq5\|1bq5]], [[1gs6\|1gs6]], [[1gs8\|1gs8]], [[1hau\|1hau]], [[1haw\|1haw]], [[1ndt\|1ndt]], [[1oe3\|1oe3]], [[1wa0\|1wa0]], [[1wa2\|1wa2]], [[2jfc\|2jfc]], [[1gs7\|1gs7]], [[1oe1\|1oe1]], [[1oe2\|1oe2]], [[1wa1\|1wa1]], [[1wae\|1wae]], [[2bo0\|2bo0]], [[2bp0\|2bp0]], [[2bp8\|2bp8]], [[2vm3\|2vm3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bq5\|1bq5]], [[1gs6\|1gs6]], [[1gs8\|1gs8]], [[1hau\|1hau]], [[1haw\|1haw]], [[1ndt\|1ndt]], [[1oe3\|1oe3]], [[1wa0\|1wa0]], [[1wa2\|1wa2]], [[2jfc\|2jfc]], [[1gs7\|1gs7]], [[1oe1\|1oe1]], [[1oe2\|1oe2]], [[1wa1\|1wa1]], [[1wae\|1wae]], [[2bo0\|2bo0]], [[2bp0\|2bp0]], [[2bp8\|2bp8]], [[2vm3\|2vm3]]</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=2vm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vm4 OCA], [http://pdbe.org/2vm4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vm4 RCSB], [http://www.ebi.ac.uk/pdbsum/2vm4 PDBsum]</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=2vm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vm4 OCA], [http://pdbe.org/2vm4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vm4 RCSB], [http://www.ebi.ac.uk/pdbsum/2vm4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vm4 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vm/2vm4_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vm/2vm4_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 28:		Line 29:

	==See Also==		==See Also==
	*[[~~Nitric~~ reductase\|~~Nitric~~ reductase]]		*[[Nitrite reductase\|Nitrite reductase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 01:10, 9 February 2016

2016-02-09T01:10:34Z

← Older revision		Revision as of 01:10, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='2vm4' size='340' side='right' caption='[[2vm4]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2vm4' size='340' side='right' caption='[[2vm4]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2vm4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Achromobacter_xylosoxidans Achromobacter~~ xylosoxidans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VM4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VM4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2vm4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_xylosoxidans"_yabuuchi_and_ohyama_1971 "achromobacter xylosoxidans" yabuuchi and ohyama 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VM4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VM4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bq5\|1bq5]], [[1gs6\|1gs6]], [[1gs8\|1gs8]], [[1hau\|1hau]], [[1haw\|1haw]], [[1ndt\|1ndt]], [[1oe3\|1oe3]], [[1wa0\|1wa0]], [[1wa2\|1wa2]], [[2jfc\|2jfc]], [[1gs7\|1gs7]], [[1oe1\|1oe1]], [[1oe2\|1oe2]], [[1wa1\|1wa1]], [[1wae\|1wae]], [[2bo0\|2bo0]], [[2bp0\|2bp0]], [[2bp8\|2bp8]], [[2vm3\|2vm3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bq5\|1bq5]], [[1gs6\|1gs6]], [[1gs8\|1gs8]], [[1hau\|1hau]], [[1haw\|1haw]], [[1ndt\|1ndt]], [[1oe3\|1oe3]], [[1wa0\|1wa0]], [[1wa2\|1wa2]], [[2jfc\|2jfc]], [[1gs7\|1gs7]], [[1oe1\|1oe1]], [[1oe2\|1oe2]], [[1wa1\|1wa1]], [[1wae\|1wae]], [[2bo0\|2bo0]], [[2bp0\|2bp0]], [[2bp8\|2bp8]], [[2vm3\|2vm3]]</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=2vm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vm4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vm4 RCSB], [http://www.ebi.ac.uk/pdbsum/2vm4 PDBsum]</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=2vm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vm4 OCA], [http://pdbe.org/2vm4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vm4 RCSB], [http://www.ebi.ac.uk/pdbsum/2vm4 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 15:		Line 15:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2vm4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 25:		Line 25:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2vm4" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Achromobacter xylosoxidans]]		[[Category: Achromobacter xylosoxidans yabuuchi and ohyama 1971]]
	[[Category: Antonyuk, S V]]		[[Category: Antonyuk, S V]]
	[[Category: Eady, R R]]		[[Category: Eady, R R]]

OCA at 15:34, 19 January 2015

2015-01-19T15:34:50Z

← Older revision		Revision as of 15:34, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2vm4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Achromobacter_xylosoxidans Achromobacter xylosoxidans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VM4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VM4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2vm4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Achromobacter_xylosoxidans Achromobacter xylosoxidans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VM4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VM4 FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bq5\|1bq5]], [[1gs6\|1gs6]], [[1gs8\|1gs8]], [[1hau\|1hau]], [[1haw\|1haw]], [[1ndt\|1ndt]], [[1oe3\|1oe3]], [[1wa0\|1wa0]], [[1wa2\|1wa2]], [[2jfc\|2jfc]], [[1gs7\|1gs7]], [[1oe1\|1oe1]], [[1oe2\|1oe2]], [[1wa1\|1wa1]], [[1wae\|1wae]], [[2bo0\|2bo0]], [[2bp0\|2bp0]], [[2bp8\|2bp8]], [[2vm3\|2vm3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bq5\|1bq5]], [[1gs6\|1gs6]], [[1gs8\|1gs8]], [[1hau\|1hau]], [[1haw\|1haw]], [[1ndt\|1ndt]], [[1oe3\|1oe3]], [[1wa0\|1wa0]], [[1wa2\|1wa2]], [[2jfc\|2jfc]], [[1gs7\|1gs7]], [[1oe1\|1oe1]], [[1oe2\|1oe2]], [[1wa1\|1wa1]], [[1wae\|1wae]], [[2bo0\|2bo0]], [[2bp0\|2bp0]], [[2bp8\|2bp8]], [[2vm3\|2vm3]]</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vm4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vm4 RCSB], [http://www.ebi.ac.uk/pdbsum/2vm4 PDBsum]</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=2vm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vm4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vm4 RCSB], [http://www.ebi.ac.uk/pdbsum/2vm4 PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Achromobacter xylosoxidans]]		[[Category: Achromobacter xylosoxidans]]
	[[Category: Antonyuk, S V.]]		[[Category: Antonyuk, S V]]
	[[Category: Eady, R R.]]		[[Category: Eady, R R]]
	[[Category: Hasnain, S S.]]		[[Category: Hasnain, S S]]
	[[Category: Hough, M A.]]		[[Category: Hough, M A]]
	[[Category: Strange, R W.]]		[[Category: Strange, R W]]
	[[Category: Denitrification]]		[[Category: Denitrification]]
	[[Category: Nitrite reductase]]		[[Category: Nitrite reductase]]
	[[Category: Ordered mechanism]]		[[Category: Ordered mechanism]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 07:47, 29 September 2014

2014-09-29T07:47:35Z

← Older revision		Revision as of 07:47, 29 September 2014
Line 1:		Line 1:
	[[Image:~~2vm4~~.~~png~~\|~~left~~\|~~200px~~]]		==STRUCTURE OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE IN SPACE GROUP R3 - 2 OF 2==
			<StructureSection load='2vm4' size='340' side='right' caption='[[2vm4]], [[Resolution\|resolution]] 1.90Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2vm4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Achromobacter_xylosoxidans Achromobacter xylosoxidans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VM4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VM4 FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bq5\|1bq5]], [[1gs6\|1gs6]], [[1gs8\|1gs8]], [[1hau\|1hau]], [[1haw\|1haw]], [[1ndt\|1ndt]], [[1oe3\|1oe3]], [[1wa0\|1wa0]], [[1wa2\|1wa2]], [[2jfc\|2jfc]], [[1gs7\|1gs7]], [[1oe1\|1oe1]], [[1oe2\|1oe2]], [[1wa1\|1wa1]], [[1wae\|1wae]], [[2bo0\|2bo0]], [[2bp0\|2bp0]], [[2bp8\|2bp8]], [[2vm3\|2vm3]]</td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vm4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vm4 RCSB], [http://www.ebi.ac.uk/pdbsum/2vm4 PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vm/2vm4_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Nitrite reductases are key enzymes that perform the first committed step in the denitrification process and reduce nitrite to nitric oxide. In copper nitrite reductases, an electron is delivered from the type 1 copper (T1Cu) centre to the type 2 copper (T2Cu) centre where catalysis occurs. Despite significant structural and mechanistic studies, it remains controversial whether the substrates, nitrite, electron and proton are utilised in an ordered or random manner. We have used crystallography, together with online X-ray absorption spectroscopy and optical spectroscopy, to show that X-rays rapidly and selectively photoreduce the T1Cu centre, but that the T2Cu centre does not photoreduce directly over a typical crystallographic data collection time. Furthermore, internal electron transfer between the T1Cu and T2Cu centres does not occur, and the T2Cu centre remains oxidised. These data unambiguously demonstrate an 'ordered' mechanism in which electron transfer is gated by binding of nitrite to the T2Cu. Furthermore, the use of online multiple spectroscopic techniques shows their value in assessing radiation-induced redox changes at different metal sites and demonstrates the importance of ensuring the correct status of redox centres in a crystal structure determination. Here, optical spectroscopy has shown a very high sensitivity for detecting the change in T1Cu redox state, while X-ray absorption spectroscopy has reported on the redox status of the T2Cu site, as this centre has no detectable optical absorption.

	~~{{STRUCTURE_2vm4\| PDB=2vm4 \| SCENE= }}~~		Crystallography with online optical and X-ray absorption spectroscopies demonstrates an ordered mechanism in copper nitrite reductase.,Hough MA, Antonyuk SV, Strange RW, Eady RR, Hasnain SS J Mol Biol. 2008 Apr 25;378(2):353-61. Epub 2008 Feb 12. PMID:18353369<ref>PMID:18353369</ref>

	~~===STRUCTURE OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE IN SPACE GROUP R3 - 2 OF 2===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18353369}}~~

	~~==About this Structure==~~
	~~[[2vm4]] is~~ a ~~1 chain structure with sequence from [http://en.wikipedia~~.~~org/wiki/Achromobacter_xylosoxidans Achromobacter xylosoxidans]~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann.ac.il/oca-bin~~/~~ocashort?id=2VM4 OCA].~~

	==See Also==		==See Also==
	*[[Nitric reductase\|Nitric reductase]]		*[[Nitric reductase\|Nitric reductase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:018353369<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Achromobacter xylosoxidans]]		[[Category: Achromobacter xylosoxidans]]
	[[Category: Antonyuk, S V.]]		[[Category: Antonyuk, S V.]]

OCA at 12:07, 20 October 2012

2012-10-20T12:07:19Z

← Older revision		Revision as of 12:07, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2vm4]] is a 1 chain structure ~~of [[Nitric reductase]]~~ with sequence from [http://en.wikipedia.org/wiki/Achromobacter_xylosoxidans Achromobacter xylosoxidans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VM4 OCA].		[[2vm4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Achromobacter_xylosoxidans Achromobacter xylosoxidans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VM4 OCA].

	==See Also==		==See Also==

OCA: Protected "2vm4" [edit=sysop:move=sysop]

2012-07-26T07:40:57Z

Protected "2vm4" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:40, 26 July 2012
(No difference)

OCA at 07:40, 26 July 2012

2012-07-26T07:40:55Z

← Older revision		Revision as of 07:40, 26 July 2012
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:2vm4.png\|left\|200px]]		[[Image:2vm4.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2vm4", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2vm4\| PDB=2vm4 \| SCENE= }}		{{STRUCTURE_2vm4\| PDB=2vm4 \| SCENE= }}

	===STRUCTURE OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE IN SPACE GROUP R3 - 2 OF 2===		===STRUCTURE OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE IN SPACE GROUP R3 - 2 OF 2===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_18353369}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 18353369 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_18353369}}		{{ABSTRACT_PUBMED_18353369}}

	==About this Structure==		==About this Structure==
	~~2VM4~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Achromobacter_xylosoxidans Achromobacter xylosoxidans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VM4 OCA].		[[2vm4]] is a 1 chain structure of [[Nitric reductase]] with sequence from [http://en.wikipedia.org/wiki/Achromobacter_xylosoxidans Achromobacter xylosoxidans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VM4 OCA].

			==See Also==
			*[[Nitric reductase\|Nitric reductase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~18353369~~</ref><references group="xtra"/>		<ref group="xtra">PMID:018353369</ref><references group="xtra"/>
	[[Category: Achromobacter xylosoxidans]]		[[Category: Achromobacter xylosoxidans]]
	[[Category: Antonyuk, S V.]]		[[Category: Antonyuk, S V.]]
Line 34:		Line 25:
	[[Category: Ordered mechanism]]		[[Category: Ordered mechanism]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 30 08:52:12 2009''~~