2fjs - Revision history

OCA at 09:27, 30 August 2023

2023-08-30T09:27:53Z

←Older revision		Revision as of 09:27, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2fjs' size='340' side='right'caption='[[2fjs]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='2fjs' size='340' side='right'caption='[[2fjs]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2fjs]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Alcfa Alcfa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FJS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FJS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2fjs]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FJS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FJS 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=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.85Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1aq8\|1aq8]], [[1as7\|1as7]], [[1as8\|1as8]]</div></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=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 ALCFA])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=2fjs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fjs OCA], [https://pdbe.org/2fjs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fjs RCSB], [https://www.ebi.ac.uk/pdbsum/2fjs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fjs 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=2fjs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fjs OCA], [https://pdbe.org/2fjs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fjs RCSB], [https://www.ebi.ac.uk/pdbsum/2fjs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fjs ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/NIR_ALCFA NIR_ALCFA]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Alcfa~~]]	+	[[Category: Alcaligenes faecalis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Murphy~~, M E.P~~]]	+	[[Category: Murphy MEP]]
-	[[Category: Tocheva~~, E I]]~~	+	[[Category: Tocheva EI]]
-	~~[[Category: Blue copper protein]]~~	+
-	~~[[Category: Cupredoxin fold]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 15:27, 3 March 2021

2021-03-03T15:27:56Z

←Older revision		Revision as of 15:27, 3 March 2021
Line 1:		Line 1:

	==Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase from A. faecalis==		==Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase from A. faecalis==
-	<StructureSection load='2fjs' size='340' side='right' caption='[[2fjs]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='2fjs' size='340' side='right'caption='[[2fjs]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2fjs]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Alcfa Alcfa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FJS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2FJS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2fjs]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcfa Alcfa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FJS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FJS 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=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aq8\|1aq8]], [[1as7\|1as7]], [[1as8\|1as8]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1aq8\|1aq8]], [[1as7\|1as7]], [[1as8\|1as8]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 ALCFA])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 ALCFA])</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'>[https://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [https://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=2fjs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fjs OCA], [~~http~~://pdbe.org/2fjs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2fjs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2fjs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2fjs 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=2fjs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fjs OCA], [https://pdbe.org/2fjs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fjs RCSB], [https://www.ebi.ac.uk/pdbsum/2fjs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fjs ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fj/2fjs_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fj/2fjs_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 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2fjs" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2fjs" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitrite reductase 3D structures\|Nitrite reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Alcfa]]		[[Category: Alcfa]]
		+	[[Category: Large Structures]]
	[[Category: Murphy, M E.P]]		[[Category: Murphy, M E.P]]
	[[Category: Tocheva, E I]]		[[Category: Tocheva, E I]]

OCA at 07:39, 18 October 2017

2017-10-18T07:39:56Z

←Older revision		Revision as of 07:39, 18 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase from A. faecalis==		==Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase from A. faecalis==
	<StructureSection load='2fjs' size='340' side='right' caption='[[2fjs]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='2fjs' size='340' side='right' caption='[[2fjs]], [[Resolution\|resolution]] 1.85Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 ALCFA])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 ALCFA])</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=2fjs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fjs OCA], [http://pdbe.org/2fjs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fjs RCSB], [http://www.ebi.ac.uk/pdbsum/2fjs 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=2fjs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fjs OCA], [http://pdbe.org/2fjs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fjs RCSB], [http://www.ebi.ac.uk/pdbsum/2fjs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2fjs ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2fjs" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2fjs" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Nitric reductase\|Nitric reductase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:57, 9 February 2016

2016-02-09T12:57:58Z

←Older revision		Revision as of 12:57, 9 February 2016
Line 17:		Line 17:
	<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=2fjs ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:28, 10 September 2015

2015-09-10T22:28:55Z

←Older revision		Revision as of 22:28, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2fjs' size='340' side='right' caption='[[2fjs]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='2fjs' size='340' side='right' caption='[[2fjs]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2fjs]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Alcaligenes_faecalis Alcaligenes faecalis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FJS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2fjs]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcfa Alcfa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FJS 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=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</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=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aq8\|1aq8]], [[1as7\|1as7]], [[1as8\|1as8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aq8\|1aq8]], [[1as7\|1as7]], [[1as8\|1as8]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 ~~Alcaligenes faecalis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 ALCFA])</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=2fjs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fjs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fjs RCSB], [http://www.ebi.ac.uk/pdbsum/2fjs 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=2fjs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fjs OCA], [http://pdbe.org/2fjs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fjs RCSB], [http://www.ebi.ac.uk/pdbsum/2fjs PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	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 2fjs" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Alcaligenes faecalis~~]]	+	[[Category: Alcfa]]
	[[Category: Murphy, M E.P]]		[[Category: Murphy, M E.P]]
	[[Category: Tocheva, E I]]		[[Category: Tocheva, E I]]

OCA at 08:10, 16 January 2015

2015-01-16T08:10:37Z

←Older revision		Revision as of 08:10, 16 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fjs]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FJS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fjs]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FJS FirstGlance]. <br>
-	</td></tr><tr><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=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene><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=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aq8\|1aq8]], [[1as7\|1as7]], [[1as8\|1as8]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aq8\|1aq8]], [[1as7\|1as7]], [[1as8\|1as8]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 Alcaligenes faecalis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 Alcaligenes faecalis])</td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fjs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fjs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fjs RCSB], [http://www.ebi.ac.uk/pdbsum/2fjs 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=2fjs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fjs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fjs RCSB], [http://www.ebi.ac.uk/pdbsum/2fjs 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 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Alcaligenes faecalis]]		[[Category: Alcaligenes faecalis]]
-	[[Category: Murphy, M E.P.]]	+	[[Category: Murphy, M E.P]]
-	[[Category: Tocheva, E I.]]	+	[[Category: Tocheva, E I]]
	[[Category: Blue copper protein]]		[[Category: Blue copper protein]]
	[[Category: Cupredoxin fold]]		[[Category: Cupredoxin fold]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 02:17, 29 September 2014

2014-09-29T02:17:03Z

←Older revision		Revision as of 02:17, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2fjs.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase from A. faecalis==
		+	<StructureSection load='2fjs' size='340' side='right' caption='[[2fjs]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2fjs]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FJS FirstGlance]. <br>
		+	</td></tr><tr><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=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aq8\|1aq8]], [[1as7\|1as7]], [[1as8\|1as8]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 Alcaligenes faecalis])</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fjs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fjs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fjs RCSB], [http://www.ebi.ac.uk/pdbsum/2fjs 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/fj/2fjs_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 ==
		+	Copper-containing nitrite reductase harbors a type-1 and a type-2 Cu site. The former acts as the electron acceptor site of the enzyme, and the latter is the site of catalytic action. The effect of the methionine ligand on the reorganization energy of the type-1 site was explored by studying the electron-transfer kinetics between NiR (wild type (wt) and the variants Met150Gly and Met150Thr) with Fe(II)EDTA and Fe(II)HEDTA. The mutations increased the reorganization energy by 0.3 eV (30 kJ mol-1). A similar increase was found from pulse radiolysis experiments on the wt NIR and three variants (Met150Gly, Met150His, and Met150Thr). Binding of the nearby Met62 to the type-1 Cu site in Met150Gly (under influence of an allosteric effector) lowered the reorganization energy back to approximately the wt value. According to XRD data the structure of the reduced type-1 site in Met150Gly NiR in the presence of an allosteric effector is similar to that in the reduced wt NiR (solved to 1.85 A), compatible with the similarity in reorganization energy.

-	~~{{STRUCTURE_2fjs\| PDB=2fjs \| SCENE= }}~~	+	Effect of the methionine ligand on the reorganization energy of the type-1 copper site of nitrite reductase.,Wijma HJ, MacPherson I, Farver O, Tocheva EI, Pecht I, Verbeet MP, Murphy ME, Canters GW J Am Chem Soc. 2007 Jan 24;129(3):519-25. PMID:17227014<ref>PMID:17227014</ref>

-	~~===Crystal Structure~~ of ~~Anaerobically Reduced Wild Type Nitrite Reductase from A~~. ~~faecalis===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17227014}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2fjs]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FJS OCA].~~	+

	==See Also==		==See Also==
	*[[Nitric reductase\|Nitric reductase]]		*[[Nitric reductase\|Nitric reductase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017227014<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Alcaligenes faecalis]]		[[Category: Alcaligenes faecalis]]
	[[Category: Murphy, M E.P.]]		[[Category: Murphy, M E.P.]]

OCA at 13:55, 20 October 2012

2012-10-20T13:55:36Z

←Older revision		Revision as of 13:55, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2fjs]] is a 3 chain structure ~~of [[Nitric reductase]]~~ with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FJS OCA].	+	[[2fjs]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FJS OCA].

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

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

2012-07-26T13:31:39Z

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

←Older revision

Revision as of 13:31, 26 July 2012

OCA at 13:31, 26 July 2012

2012-07-26T13:31:37Z

←Older revision		Revision as of 13:31, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2fjs.png\|left\|200px]]		[[Image:2fjs.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2fjs", 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_2fjs\| PDB=2fjs \| SCENE= }}		{{STRUCTURE_2fjs\| PDB=2fjs \| SCENE= }}

	===Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase from A. faecalis===		===Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase from A. faecalis===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17227014}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17227014 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17227014}}		{{ABSTRACT_PUBMED_17227014}}

	==About this Structure==		==About this Structure==
-	~~2FJS~~ is a 3 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FJS OCA].	+	[[2fjs]] is a 3 chain structure of [[Nitric reductase]] with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FJS OCA].
		+
		+	==See Also==
		+	*[[Nitric reductase\|Nitric reductase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17227014~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017227014</ref><references group="xtra"/>
	[[Category: Alcaligenes faecalis]]		[[Category: Alcaligenes faecalis]]
	[[Category: Murphy, M E.P.]]		[[Category: Murphy, M E.P.]]
Line 29:		Line 20:
	[[Category: Blue copper protein]]		[[Category: Blue copper protein]]
	[[Category: Cupredoxin fold]]		[[Category: Cupredoxin fold]]
-		+	[[Category: Oxidoreductase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 09:58:04 2009''~~	+