2avf - Revision history

OCA at 13:42, 13 March 2024

OCA — Wed, 13 Mar 2024 13:42:05 GMT

←Older revision		Revision as of 13:42, 13 March 2024
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	<StructureSection load='2avf' size='340' side='right'caption='[[2avf]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2avf' size='340' side='right'caption='[[2avf]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2avf]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"achromobacter_cycloclastes"_(gray_and_thornton)_bergey_et_al. "achromobacter~~ cycloclastes~~" (gray and thornton) bergey et al.~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AVF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AVF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2avf]] is a 6 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=2AVF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AVF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~, ~~<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]] 2.6Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1rzp\|1rzp]], [[1rzq\|1rzq]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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=2avf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2avf OCA], [https://pdbe.org/2avf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2avf RCSB], [https://www.ebi.ac.uk/pdbsum/2avf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2avf 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=2avf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2avf OCA], [https://pdbe.org/2avf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2avf RCSB], [https://www.ebi.ac.uk/pdbsum/2avf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2avf 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]]
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	</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=2avf 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=2avf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Monoclinic crystal structure of C-terminal desundecapeptide nitrite reductase (NiRc-11) from Achromobacter cycloclastes was determined at 2.6A. NiRc-11 exists as a loose trimer in the crystal. Deletion of 11 residues eliminates all intersubunit hydrogen bonds mediated by the C-terminal tail. The rigid irregular coil 105-112, which constitutes part of the sidewall of the active site pocket, undergoes conformational changes and becomes highly flexible in NiRc-11. Correspondingly, the linker segments between the two copper sites 95-100 and 135-136 are partly relaxed in conformation, which leads to disrupted active site microenvironments responsible for the activity loss and spectral change of NiRc-11. Comparison with the native structure revealed a bulky residue Met331 fastened by hydrogen bonding, which may play a direct role in keeping the right copper site geometry by protruding its side chain against the irregular coil 105-112. Sequence alignment showed that the bulky residue is conserved at position 331, indicating an equal importance of C-terminal segment in other copper-containing nitrite reductases.
-
-	Crystal structure of C-terminal desundecapeptide nitrite reductase from Achromobacter cycloclastes.,Li HT, Chang T, Chang WC, Chen CJ, Liu MY, Gui LL, Zhang JP, An XM, Chang WR Biochem Biophys Res Commun. 2005 Dec 30;338(4):1935-42. Epub 2005 Nov 15. PMID:16293231<ref>PMID:16293231</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2avf" 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: Large Structures]]		[[Category: Large Structures]]
-	[[Category: An~~, X M~~]]	+	[[Category: An XM]]
-	[[Category: Chang, T]]	+	[[Category: Chang T]]
-	[[Category: Chang~~, W C~~]]	+	[[Category: Chang WC]]
-	[[Category: Chang~~, W R~~]]	+	[[Category: Chang WR]]
-	[[Category: Chen~~, C J~~]]	+	[[Category: Chen CJ]]
-	[[Category: Gui~~, L L~~]]	+	[[Category: Gui LL]]
-	[[Category: Li~~, H T~~]]	+	[[Category: Li HT]]
-	[[Category: Liu~~, M Y~~]]	+	[[Category: Liu MY]]
-	[[Category: Zhang~~, J P]]~~	+	[[Category: Zhang JP]]
-	~~[[Category: Beta barrel trimer]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 14:45, 17 November 2021

OCA — Wed, 17 Nov 2021 14:45:39 GMT

←Older revision		Revision as of 14:45, 17 November 2021
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	<StructureSection load='2avf' size='340' side='right'caption='[[2avf]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2avf' size='340' side='right'caption='[[2avf]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2avf]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"achromobacter_cycloclastes"_(gray_and_thornton)_bergey_et_al. "achromobacter cycloclastes" (gray and thornton) bergey et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AVF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2AVF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2avf]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"achromobacter_cycloclastes"_(gray_and_thornton)_bergey_et_al. "achromobacter cycloclastes" (gray and thornton) bergey et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AVF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AVF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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=CL:CHLORIDE+ION'>CL</scene>, <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">[[1rzp\|1rzp]], [[1rzq\|1rzq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1rzp\|1rzp]], [[1rzq\|1rzq]]</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=2avf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2avf OCA], [~~http~~://pdbe.org/2avf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2avf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2avf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2avf 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=2avf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2avf OCA], [https://pdbe.org/2avf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2avf RCSB], [https://www.ebi.ac.uk/pdbsum/2avf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2avf ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 05:21, 13 February 2020

OCA — Thu, 13 Feb 2020 05:21:42 GMT

←Older revision		Revision as of 05:21, 13 February 2020
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	==Crystal Structure of C-terminal Desundecapeptide Nitrite Reductase from Achromobacter cycloclastes==		==Crystal Structure of C-terminal Desundecapeptide Nitrite Reductase from Achromobacter cycloclastes==
-	<StructureSection load='2avf' size='340' side='right' caption='[[2avf]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='2avf' size='340' side='right'caption='[[2avf]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2avf]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_cycloclastes"_(gray_and_thornton)_bergey_et_al. "achromobacter cycloclastes" (gray and thornton) bergey et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AVF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AVF FirstGlance]. <br>		<table><tr><td colspan='2'>[[2avf]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_cycloclastes"_(gray_and_thornton)_bergey_et_al. "achromobacter cycloclastes" (gray and thornton) bergey et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AVF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AVF FirstGlance]. <br>
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Nitrite reductase\|Nitrite reductase]]	+	*[[Nitrite reductase 3D structures\|Nitrite reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: An, X M]]		[[Category: An, X M]]
	[[Category: Chang, T]]		[[Category: Chang, T]]

OCA at 07:12, 9 May 2018

OCA — Wed, 09 May 2018 07:12:59 GMT

←Older revision		Revision as of 07:12, 9 May 2018
Line 1:		Line 1:
		+
	==Crystal Structure of C-terminal Desundecapeptide Nitrite Reductase from Achromobacter cycloclastes==		==Crystal Structure of C-terminal Desundecapeptide Nitrite Reductase from Achromobacter cycloclastes==
	<StructureSection load='2avf' size='340' side='right' caption='[[2avf]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2avf' size='340' side='right' caption='[[2avf]], [[Resolution\|resolution]] 2.60Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rzp\|1rzp]], [[1rzq\|1rzq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rzp\|1rzp]], [[1rzq\|1rzq]]</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=2avf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2avf OCA], [http://pdbe.org/2avf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2avf RCSB], [http://www.ebi.ac.uk/pdbsum/2avf 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=2avf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2avf OCA], [http://pdbe.org/2avf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2avf RCSB], [http://www.ebi.ac.uk/pdbsum/2avf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2avf 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/av/2avf_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/av/2avf_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>
	</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=2avf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:

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

OCA at 16:59, 11 September 2015

OCA — Fri, 11 Sep 2015 16:59:01 GMT

←Older revision		Revision as of 16:59, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2avf' size='340' side='right' caption='[[2avf]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2avf' size='340' side='right' caption='[[2avf]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2avf]] is a 6 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=2AVF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AVF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2avf]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_cycloclastes"_(gray_and_thornton)_bergey_et_al. "achromobacter cycloclastes" (gray and thornton) bergey et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AVF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AVF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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">[[1rzp\|1rzp]], [[1rzq\|1rzq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rzp\|1rzp]], [[1rzq\|1rzq]]</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=2avf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2avf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2avf RCSB], [http://www.ebi.ac.uk/pdbsum/2avf 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=2avf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2avf OCA], [http://pdbe.org/2avf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2avf RCSB], [http://www.ebi.ac.uk/pdbsum/2avf PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	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 2avf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Achromobacter cycloclastes]]
	[[Category: An, X M]]		[[Category: An, X M]]
	[[Category: Chang, T]]		[[Category: Chang, T]]

OCA at 09:33, 8 January 2015

OCA — Thu, 08 Jan 2015 09:33:42 GMT

←Older revision		Revision as of 09:33, 8 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2avf]] is a 6 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=2AVF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AVF FirstGlance]. <br>		<table><tr><td colspan='2'>[[2avf]] is a 6 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=2AVF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AVF FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rzp\|1rzp]], [[1rzq\|1rzq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rzp\|1rzp]], [[1rzq\|1rzq]]</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=2avf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2avf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2avf RCSB], [http://www.ebi.ac.uk/pdbsum/2avf 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=2avf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2avf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2avf RCSB], [http://www.ebi.ac.uk/pdbsum/2avf 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: An, X M.]]	+	[[Category: An, X M]]
-	[[Category: Chang, T.]]	+	[[Category: Chang, T]]
-	[[Category: Chang, W C.]]	+	[[Category: Chang, W C]]
-	[[Category: Chang, W R.]]	+	[[Category: Chang, W R]]
-	[[Category: Chen, C J.]]	+	[[Category: Chen, C J]]
-	[[Category: Gui, L L.]]	+	[[Category: Gui, L L]]
-	[[Category: Li, H T.]]	+	[[Category: Li, H T]]
-	[[Category: Liu, M Y.]]	+	[[Category: Liu, M Y]]
-	[[Category: Zhang, J P.]]	+	[[Category: Zhang, J P]]
	[[Category: Beta barrel trimer]]		[[Category: Beta barrel trimer]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 02:31, 29 September 2014

OCA — Mon, 29 Sep 2014 02:31:18 GMT

←Older revision		Revision as of 02:31, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2avf.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of C-terminal Desundecapeptide Nitrite Reductase from Achromobacter cycloclastes==
		+	<StructureSection load='2avf' size='340' side='right' caption='[[2avf]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2avf]] is a 6 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=2AVF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AVF FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rzp\|1rzp]], [[1rzq\|1rzq]]</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=2avf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2avf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2avf RCSB], [http://www.ebi.ac.uk/pdbsum/2avf 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/av/2avf_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 ==
		+	Monoclinic crystal structure of C-terminal desundecapeptide nitrite reductase (NiRc-11) from Achromobacter cycloclastes was determined at 2.6A. NiRc-11 exists as a loose trimer in the crystal. Deletion of 11 residues eliminates all intersubunit hydrogen bonds mediated by the C-terminal tail. The rigid irregular coil 105-112, which constitutes part of the sidewall of the active site pocket, undergoes conformational changes and becomes highly flexible in NiRc-11. Correspondingly, the linker segments between the two copper sites 95-100 and 135-136 are partly relaxed in conformation, which leads to disrupted active site microenvironments responsible for the activity loss and spectral change of NiRc-11. Comparison with the native structure revealed a bulky residue Met331 fastened by hydrogen bonding, which may play a direct role in keeping the right copper site geometry by protruding its side chain against the irregular coil 105-112. Sequence alignment showed that the bulky residue is conserved at position 331, indicating an equal importance of C-terminal segment in other copper-containing nitrite reductases.

-	~~{{STRUCTURE_2avf\| PDB=2avf \| SCENE= }}~~	+	Crystal structure of C-terminal desundecapeptide nitrite reductase from Achromobacter cycloclastes.,Li HT, Chang T, Chang WC, Chen CJ, Liu MY, Gui LL, Zhang JP, An XM, Chang WR Biochem Biophys Res Commun. 2005 Dec 30;338(4):1935-42. Epub 2005 Nov 15. PMID:16293231<ref>PMID:16293231</ref>

-	~~===Crystal Structure~~ of ~~C-terminal Desundecapeptide Nitrite Reductase from Achromobacter cycloclastes===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16293231}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2avf]] is a 6 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=2AVF OCA].~~	+

	==See Also==		==See Also==
	*[[Nitric reductase\|Nitric reductase]]		*[[Nitric reductase\|Nitric reductase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:016293231<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Achromobacter cycloclastes]]		[[Category: Achromobacter cycloclastes]]
	[[Category: An, X M.]]		[[Category: An, X M.]]

OCA at 20:28, 20 October 2012

OCA — Sat, 20 Oct 2012 20:28:26 GMT

←Older revision		Revision as of 20:28, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2avf]] is a 6 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=2AVF OCA].	+	[[2avf]] is a 6 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=2AVF OCA].

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

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

OCA — Fri, 27 Jul 2012 10:35:24 GMT

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

←Older revision

Revision as of 10:35, 27 July 2012

OCA at 10:35, 27 July 2012

OCA — Fri, 27 Jul 2012 10:35:23 GMT

←Older revision		Revision as of 10:35, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2avf.png\|left\|200px]]		[[Image:2avf.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2avf", 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.
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	{{STRUCTURE_2avf\| PDB=2avf \| SCENE= }}		{{STRUCTURE_2avf\| PDB=2avf \| SCENE= }}

	===Crystal Structure of C-terminal Desundecapeptide Nitrite Reductase from Achromobacter cycloclastes===		===Crystal Structure of C-terminal Desundecapeptide Nitrite Reductase from Achromobacter cycloclastes===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16293231}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16293231 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16293231}}		{{ABSTRACT_PUBMED_16293231}}

	==About this Structure==		==About this Structure==
-	~~2AVF~~ is a 6 ~~chains~~ structure of ~~sequences~~ 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=2AVF OCA].	+	[[2avf]] is a 6 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=2AVF OCA].
		+
		+	==See Also==
		+	*[[Nitric reductase\|Nitric reductase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16293231~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016293231</ref><references group="xtra"/>
	[[Category: Achromobacter cycloclastes]]		[[Category: Achromobacter cycloclastes]]
	[[Category: An, X M.]]		[[Category: An, X M.]]
Line 35:		Line 26:
	[[Category: Zhang, J P.]]		[[Category: Zhang, J P.]]
	[[Category: Beta barrel trimer]]		[[Category: Beta barrel trimer]]
-		+	[[Category: Oxidoreductase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Wed Feb 18 04:17:13 2009''~~	+