1nif - Revision history

OCA at 07:56, 14 February 2024

OCA — Wed, 14 Feb 2024 07:56:57 GMT

←Older revision		Revision as of 07:56, 14 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1nif]] 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=1NIF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NIF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1nif]] 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=1NIF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NIF 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>~~</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]] 1.7Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[1nia\|1nia]], [[1nib\|1nib]], [[1nic\|1nic]], [[1nid\|1nid]], [[1nie\|1nie]], [[2nrd\|2nrd]]</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></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=1nif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nif OCA], [https://pdbe.org/1nif PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nif RCSB], [https://www.ebi.ac.uk/pdbsum/1nif PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nif 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=1nif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nif OCA], [https://pdbe.org/1nif PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nif RCSB], [https://www.ebi.ac.uk/pdbsum/1nif PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nif ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/NIR_ACHCY NIR_ACHCY]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</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=1nif 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=1nif ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	High resolution x-ray crystallographic structures of nitrite reductase from Achromobacter cycloclastes, undertaken in order to understand the pH optimum of the reaction with nitrite, show that at pH 5.0, 5.4, 6.0, 6.2, and 6.8, no significant changes occur, other than in the occupancy of the type II copper at the active site. An extensive network of hydrogen bonds, both within and between subunits of the trimer, maintains the rigidity of the protein structure. A water occupies a site approximately 1.5 A from the site of the type II copper in the structure of the type II copper-depleted structure (at pH 5.4), again with no other significant changes in structure. In nitrite-soaked crystals, nitrite binds via its oxygens to the type II copper and replaces the water normally bound to the type II copper. The active-site cavity of the protein is distinctly hydrophobic on one side and hydrophilic on the other, providing a possible path for diffusion of the product NO. Asp-98 exhibits thermal parameter values higher than its surroundings, suggesting a role in shuttling the two protons necessary for the overall reaction. The strong structural homology with cupredoxins is described.
-
-	The structure of copper-nitrite reductase from Achromobacter cycloclastes at five pH values, with NO2- bound and with type II copper depleted.,Adman ET, Godden JW, Turley S J Biol Chem. 1995 Nov 17;270(46):27458-74. PMID:7499203<ref>PMID:7499203</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1nif" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Nitrite reductase 3D structures\|Nitrite reductase 3D structures]]		*[[Nitrite reductase 3D structures\|Nitrite reductase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Achromobacter cycloclastes]]		[[Category: Achromobacter cycloclastes]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Adman~~, E T~~]]	+	[[Category: Adman ET]]
-	[[Category: Godden~~, J W~~]]	+	[[Category: Godden JW]]
-	[[Category: Turley, S]]	+	[[Category: Turley S]]

OCA at 07:03, 25 August 2021

OCA — Wed, 25 Aug 2021 07:03:11 GMT

←Older revision		Revision as of 07:03, 25 August 2021
Line 3:		Line 3:
	<StructureSection load='1nif' size='340' side='right'caption='[[1nif]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1nif' size='340' side='right'caption='[[1nif]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nif]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Achromobacter_cycloclastes Achromobacter cycloclastes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1NIF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nif]] 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=1NIF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NIF 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></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></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nia\|1nia]], [[1nib\|1nib]], [[1nic\|1nic]], [[1nid\|1nid]], [[1nie\|1nie]], [[2nrd\|2nrd]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1nia\|1nia]], [[1nib\|1nib]], [[1nic\|1nic]], [[1nid\|1nid]], [[1nie\|1nie]], [[2nrd\|2nrd]]</div></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=1nif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nif OCA], [~~http~~://pdbe.org/1nif PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1nif RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1nif PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1nif 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=1nif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nif OCA], [https://pdbe.org/1nif PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nif RCSB], [https://www.ebi.ac.uk/pdbsum/1nif PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nif ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 18:31, 20 November 2019

OCA — Wed, 20 Nov 2019 18:31:42 GMT

←Older revision		Revision as of 18:31, 20 November 2019
Line 1:		Line 1:

	==THE STRUCTURE OF CU-NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT FIVE PH VALUES, WITH NITRITE BOUND AND WITH TYPE II CU DEPLETED==		==THE STRUCTURE OF CU-NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT FIVE PH VALUES, WITH NITRITE BOUND AND WITH TYPE II CU DEPLETED==
-	<StructureSection load='1nif' size='340' side='right' caption='[[1nif]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='1nif' size='340' side='right'caption='[[1nif]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1nif]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Achromobacter_cycloclastes Achromobacter cycloclastes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NIF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1nif]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Achromobacter_cycloclastes Achromobacter cycloclastes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NIF FirstGlance]. <br>
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1nif" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1nif" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitrite reductase 3D structures\|Nitrite reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Achromobacter cycloclastes]]		[[Category: Achromobacter cycloclastes]]
		+	[[Category: Large Structures]]
	[[Category: Adman, E T]]		[[Category: Adman, E T]]
	[[Category: Godden, J W]]		[[Category: Godden, J W]]
	[[Category: Turley, S]]		[[Category: Turley, S]]

OCA at 07:18, 7 February 2018

OCA — Wed, 07 Feb 2018 07:18:47 GMT

←Older revision		Revision as of 07:18, 7 February 2018
Line 1:		Line 1:
		+
	==THE STRUCTURE OF CU-NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT FIVE PH VALUES, WITH NITRITE BOUND AND WITH TYPE II CU DEPLETED==		==THE STRUCTURE OF CU-NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT FIVE PH VALUES, WITH NITRITE BOUND AND WITH TYPE II CU DEPLETED==
	<StructureSection load='1nif' size='340' side='right' caption='[[1nif]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1nif' size='340' side='right' caption='[[1nif]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nia\|1nia]], [[1nib\|1nib]], [[1nic\|1nic]], [[1nid\|1nid]], [[1nie\|1nie]], [[2nrd\|2nrd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nia\|1nia]], [[1nib\|1nib]], [[1nic\|1nic]], [[1nid\|1nid]], [[1nie\|1nie]], [[2nrd\|2nrd]]</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=1nif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nif OCA], [http://pdbe.org/1nif PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nif RCSB], [http://www.ebi.ac.uk/pdbsum/1nif 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=1nif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nif OCA], [http://pdbe.org/1nif PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nif RCSB], [http://www.ebi.ac.uk/pdbsum/1nif PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nif ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ni/1nif_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ni/1nif_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 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1nif" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1nif" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Nitric reductase\|Nitric reductase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 01:13, 9 February 2016

OCA — Tue, 09 Feb 2016 01:13:06 GMT

←Older revision		Revision as of 01:13, 9 February 2016
Line 16:		Line 16:
	<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=1nif ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:10, 10 September 2015

OCA — Thu, 10 Sep 2015 17:10:14 GMT

←Older revision		Revision as of 17:10, 10 September 2015
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nia\|1nia]], [[1nib\|1nib]], [[1nic\|1nic]], [[1nid\|1nid]], [[1nie\|1nie]], [[2nrd\|2nrd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nia\|1nia]], [[1nib\|1nib]], [[1nic\|1nic]], [[1nid\|1nid]], [[1nie\|1nie]], [[2nrd\|2nrd]]</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=1nif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nif OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nif RCSB], [http://www.ebi.ac.uk/pdbsum/1nif 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=1nif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nif OCA], [http://pdbe.org/1nif PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nif RCSB], [http://www.ebi.ac.uk/pdbsum/1nif PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 1nif" style="background-color:#fffaf0;"></div>

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

OCA at 16:44, 5 January 2015

OCA — Mon, 05 Jan 2015 16:44:44 GMT

←Older revision		Revision as of 16:44, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1nif]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Achromobacter_cycloclastes Achromobacter cycloclastes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NIF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1nif]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Achromobacter_cycloclastes Achromobacter cycloclastes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NIF 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><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></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nia\|1nia]], [[1nib\|1nib]], [[1nic\|1nic]], [[1nid\|1nid]], [[1nie\|1nie]], [[2nrd\|2nrd]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nia\|1nia]], [[1nib\|1nib]], [[1nic\|1nic]], [[1nid\|1nid]], [[1nie\|1nie]], [[2nrd\|2nrd]]</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=1nif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nif OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nif RCSB], [http://www.ebi.ac.uk/pdbsum/1nif 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=1nif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nif OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nif RCSB], [http://www.ebi.ac.uk/pdbsum/1nif 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 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Achromobacter cycloclastes]]		[[Category: Achromobacter cycloclastes]]
-	[[Category: Adman, E T.]]	+	[[Category: Adman, E T]]
-	[[Category: Godden, J W.]]	+	[[Category: Godden, J W]]
-	[[Category: Turley, S.]]	+	[[Category: Turley, S]]

OCA at 13:53, 28 September 2014

OCA — Sun, 28 Sep 2014 13:53:42 GMT

←Older revision		Revision as of 13:53, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1nif.~~png~~\|~~left~~\|200px]]	+	==THE STRUCTURE OF CU-NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT FIVE PH VALUES, WITH NITRITE BOUND AND WITH TYPE II CU DEPLETED==
		+	<StructureSection load='1nif' size='340' side='right' caption='[[1nif]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1nif]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Achromobacter_cycloclastes Achromobacter cycloclastes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NIF 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><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nia\|1nia]], [[1nib\|1nib]], [[1nic\|1nic]], [[1nid\|1nid]], [[1nie\|1nie]], [[2nrd\|2nrd]]</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=1nif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nif OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nif RCSB], [http://www.ebi.ac.uk/pdbsum/1nif 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/ni/1nif_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 ==
		+	High resolution x-ray crystallographic structures of nitrite reductase from Achromobacter cycloclastes, undertaken in order to understand the pH optimum of the reaction with nitrite, show that at pH 5.0, 5.4, 6.0, 6.2, and 6.8, no significant changes occur, other than in the occupancy of the type II copper at the active site. An extensive network of hydrogen bonds, both within and between subunits of the trimer, maintains the rigidity of the protein structure. A water occupies a site approximately 1.5 A from the site of the type II copper in the structure of the type II copper-depleted structure (at pH 5.4), again with no other significant changes in structure. In nitrite-soaked crystals, nitrite binds via its oxygens to the type II copper and replaces the water normally bound to the type II copper. The active-site cavity of the protein is distinctly hydrophobic on one side and hydrophilic on the other, providing a possible path for diffusion of the product NO. Asp-98 exhibits thermal parameter values higher than its surroundings, suggesting a role in shuttling the two protons necessary for the overall reaction. The strong structural homology with cupredoxins is described.

-	~~{{STRUCTURE_1nif\| PDB=1nif \| SCENE= }}~~	+	The structure of copper-nitrite reductase from Achromobacter cycloclastes at five pH values, with NO2- bound and with type II copper depleted.,Adman ET, Godden JW, Turley S J Biol Chem. 1995 Nov 17;270(46):27458-74. PMID:7499203<ref>PMID:7499203</ref>

-	~~===THE STRUCTURE OF CU-NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT FIVE PH VALUES~~, ~~WITH NITRITE BOUND AND WITH TYPE II CU DEPLETED===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_7499203}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1nif]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Achromobacter_cycloclastes Achromobacter cycloclastes]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1NIF OCA].~~	+

	==See Also==		==See Also==
	*[[Nitric reductase\|Nitric reductase]]		*[[Nitric reductase\|Nitric reductase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:007499203<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Achromobacter cycloclastes]]		[[Category: Achromobacter cycloclastes]]
	[[Category: Adman, E T.]]		[[Category: Adman, E T.]]
	[[Category: Godden, J W.]]		[[Category: Godden, J W.]]
	[[Category: Turley, S.]]		[[Category: Turley, S.]]

OCA at 12:07, 20 October 2012

OCA — Sat, 20 Oct 2012 12:07:37 GMT

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

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

	==See Also==		==See Also==
Line 14:		Line 14:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:007499203~~</ref><ref group="xtra">PMID:011917145~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:007499203</ref><references group="xtra"/>
	[[Category: Achromobacter cycloclastes]]		[[Category: Achromobacter cycloclastes]]
	[[Category: Adman, E T.]]		[[Category: Adman, E T.]]
	[[Category: Godden, J W.]]		[[Category: Godden, J W.]]
	[[Category: Turley, S.]]		[[Category: Turley, S.]]

OCA: Protected "1nif" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 07:42:10 GMT

Protected "1nif" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:42, 26 July 2012