1ibf - Revision history

OCA at 06:01, 3 April 2024

OCA — Wed, 03 Apr 2024 06:01:53 GMT

←Older revision		Revision as of 06:01, 3 April 2024
Line 3:		Line 3:
	<StructureSection load='1ibf' size='340' side='right'caption='[[1ibf]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1ibf' size='340' side='right'caption='[[1ibf]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ibf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"photobacterium_leiognathi_subsp~~._leiognathi~~"_(boisvert_et_al._1967)_ast_and_dunlap_2004 "photobacterium~~ leiognathi subsp. leiognathi~~" (boisvert et al. 1967) ast and dunlap 2004~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IBF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ibf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Photobacterium_leiognathi_subsp._leiognathi Photobacterium leiognathi subsp. leiognathi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IBF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1bzo\|1bzo]], [[1ib5\|1ib5]], [[1ibb\|1ibb]], [[1ibd\|1ibd]], [[1ibh\|1ibh]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1]~~ </~~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=1ibf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ibf OCA], [https://pdbe.org/1ibf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ibf RCSB], [https://www.ebi.ac.uk/pdbsum/1ibf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ibf 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=1ibf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ibf OCA], [https://pdbe.org/1ibf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ibf RCSB], [https://www.ebi.ac.uk/pdbsum/1ibf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ibf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SODC_PHOLE SODC_PHOLE]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.	+	[https://www.uniprot.org/uniprot/SODC_PHOLE SODC_PHOLE] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
	== 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=1ibf 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=1ibf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The functional properties and X-ray structures of five mutant forms of Photobacterium leiognathi Cu,Zn superoxide dismutase carrying single mutations at residues located at the dimer association interface have been investigated. When compared to the wild-type enzyme, the three-dimensional structures of the mutants show structural perturbations limited to the proximity of the mutation sites and substantial identity of active site geometry. Nonetheless, the catalytic rates of all mutants, measured at neutral pH and low ionic strength by pulse radiolysis, are higher than that of the wild-type protein. Such enzymatic activity increase is paralleled by enhanced active site accessibility to external chelating agents, which, in the mutated enzyme, remove more readily the active site copper ion. It is concluded that mutations at the prokaryotic Cu,Zn superoxide dismutase subunit interface can transduce dynamical perturbation to the active site region, promoting substrate active site accessibility. Such long-range intramolecular communication effects have not been extensively described before within the Cu,Zn superoxide dismutase homology family.
-
-	Single mutations at the subunit interface modulate copper reactivity in Photobacterium leiognathi Cu,Zn superoxide dismutase.,Stroppolo ME, Pesce A, D'Orazio M, O'Neill P, Bordo D, Rosano C, Milani M, Battistoni A, Bolognesi M, Desideri A J Mol Biol. 2001 May 4;308(3):555-63. PMID:11327787<ref>PMID:11327787</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ibf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Superoxide dismutase 3D structures\|Superoxide dismutase 3D structures]]		*[[Superoxide dismutase 3D structures\|Superoxide dismutase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Superoxide dismutase~~]]	+	[[Category: Photobacterium leiognathi subsp. leiognathi]]
-	[[Category: Battistoni, A]]	+	[[Category: Battistoni A]]
-	[[Category: Bolognesi, M]]	+	[[Category: Bolognesi M]]
-	[[Category: Bordo, D]]	+	[[Category: Bordo D]]
-	[[Category: ~~Desideri, A~~]]	+	[[Category: D'Orazio M]]
-	[[Category: ~~Milani, M~~]]	+	[[Category: Desideri A]]
-	[[Category: ~~Neill, P O~~]]	+	[[Category: Milani M]]
-	[[Category: ~~Orazio, M D~~]]	+	[[Category: O'Neill P]]
-	[[Category: Pesce, A]]	+	[[Category: Pesce A]]
-	[[Category: Rosano, C]]	+	[[Category: Rosano C]]
-	[[Category: Stroppolo~~, M E]]~~	+	[[Category: Stroppolo ME]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Prokaryotic superoxide dismutase]]~~	+
-	~~[[Category: Subunit interaction~~]]	+

OCA at 10:59, 4 August 2021

OCA — Wed, 04 Aug 2021 10:59:00 GMT

←Older revision		Revision as of 10:59, 4 August 2021
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	<StructureSection load='1ibf' size='340' side='right'caption='[[1ibf]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1ibf' size='340' side='right'caption='[[1ibf]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ibf]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"photobacterium_leiognathi_subsp._leiognathi"_(boisvert_et_al._1967)_ast_and_dunlap_2004 "photobacterium leiognathi subsp. leiognathi" (boisvert et al. 1967) ast and dunlap 2004]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1IBF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ibf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"photobacterium_leiognathi_subsp._leiognathi"_(boisvert_et_al._1967)_ast_and_dunlap_2004 "photobacterium leiognathi subsp. leiognathi" (boisvert et al. 1967) ast and dunlap 2004]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IBF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bzo\|1bzo]], [[1ib5\|1ib5]], [[1ibb\|1ibb]], [[1ibd\|1ibd]], [[1ibh\|1ibh]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1bzo\|1bzo]], [[1ib5\|1ib5]], [[1ibb\|1ibb]], [[1ibd\|1ibd]], [[1ibh\|1ibh]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </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=1ibf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ibf OCA], [~~http~~://pdbe.org/1ibf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ibf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ibf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ibf 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=1ibf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ibf OCA], [https://pdbe.org/1ibf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ibf RCSB], [https://www.ebi.ac.uk/pdbsum/1ibf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ibf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SODC_PHOLE SODC_PHOLE]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.	+	[[https://www.uniprot.org/uniprot/SODC_PHOLE SODC_PHOLE]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[Superoxide ~~Dismutase~~\|Superoxide ~~Dismutase~~]]	+	*[[Superoxide dismutase 3D structures\|Superoxide dismutase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:24, 30 October 2019

OCA — Wed, 30 Oct 2019 10:24:32 GMT

←Older revision		Revision as of 10:24, 30 October 2019
Line 1:		Line 1:

	==X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT V29G==		==X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT V29G==
-	<StructureSection load='1ibf' size='340' side='right' caption='[[1ibf]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='1ibf' size='340' side='right'caption='[[1ibf]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ibf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"photobacterium_leiognathi_subsp._leiognathi"_(boisvert_et_al._1967)_ast_and_dunlap_2004 "photobacterium leiognathi subsp. leiognathi" (boisvert et al. 1967) ast and dunlap 2004]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IBF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ibf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"photobacterium_leiognathi_subsp._leiognathi"_(boisvert_et_al._1967)_ast_and_dunlap_2004 "photobacterium leiognathi subsp. leiognathi" (boisvert et al. 1967) ast and dunlap 2004]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IBF FirstGlance]. <br>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1ibf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ibf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Superoxide Dismutase\|Superoxide Dismutase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]
	[[Category: Battistoni, A]]		[[Category: Battistoni, A]]

OCA at 09:25, 10 January 2018

OCA — Wed, 10 Jan 2018 09:25:18 GMT

←Older revision		Revision as of 09:25, 10 January 2018
Line 1:		Line 1:
		+
	==X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT V29G==		==X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT V29G==
	<StructureSection load='1ibf' size='340' side='right' caption='[[1ibf]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1ibf' size='340' side='right' caption='[[1ibf]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bzo\|1bzo]], [[1ib5\|1ib5]], [[1ibb\|1ibb]], [[1ibd\|1ibd]], [[1ibh\|1ibh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bzo\|1bzo]], [[1ib5\|1ib5]], [[1ibb\|1ibb]], [[1ibd\|1ibd]], [[1ibh\|1ibh]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </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=1ibf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ibf OCA], [http://pdbe.org/1ibf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ibf RCSB], [http://www.ebi.ac.uk/pdbsum/1ibf 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=1ibf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ibf OCA], [http://pdbe.org/1ibf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ibf RCSB], [http://www.ebi.ac.uk/pdbsum/1ibf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ibf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ib/1ibf_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ib/1ibf_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 30:
	</div>		</div>
	<div class="pdbe-citations 1ibf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ibf" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Superoxide Dismutase\|Superoxide Dismutase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 01:34, 9 February 2016

OCA — Tue, 09 Feb 2016 01:34:12 GMT

←Older revision		Revision as of 01:34, 9 February 2016
Line 18:		Line 18:
	<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=1ibf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:19, 10 September 2015

OCA — Thu, 10 Sep 2015 17:19:46 GMT

←Older revision		Revision as of 17:19, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1ibf' size='340' side='right' caption='[[1ibf]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1ibf' size='340' side='right' caption='[[1ibf]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ibf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Photobacterium_leiognathi Photobacterium~~ leiognathi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IBF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ibf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"photobacterium_leiognathi_subsp._leiognathi"_(boisvert_et_al._1967)_ast_and_dunlap_2004 "photobacterium leiognathi subsp. leiognathi" (boisvert et al. 1967) ast and dunlap 2004]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IBF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bzo\|1bzo]], [[1ib5\|1ib5]], [[1ibb\|1ibb]], [[1ibd\|1ibd]], [[1ibh\|1ibh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bzo\|1bzo]], [[1ib5\|1ib5]], [[1ibb\|1ibb]], [[1ibd\|1ibd]], [[1ibh\|1ibh]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </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=1ibf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ibf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ibf RCSB], [http://www.ebi.ac.uk/pdbsum/1ibf 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=1ibf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ibf OCA], [http://pdbe.org/1ibf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ibf RCSB], [http://www.ebi.ac.uk/pdbsum/1ibf PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1ibf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Photobacterium leiognathi]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]
	[[Category: Battistoni, A]]		[[Category: Battistoni, A]]

OCA at 03:31, 25 December 2014

OCA — Thu, 25 Dec 2014 03:31:17 GMT

←Older revision		Revision as of 03:31, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ibf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Photobacterium_leiognathi Photobacterium leiognathi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IBF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ibf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Photobacterium_leiognathi Photobacterium leiognathi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IBF FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bzo\|1bzo]], [[1ib5\|1ib5]], [[1ibb\|1ibb]], [[1ibd\|1ibd]], [[1ibh\|1ibh]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bzo\|1bzo]], [[1ib5\|1ib5]], [[1ibb\|1ibb]], [[1ibd\|1ibd]], [[1ibh\|1ibh]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </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=1ibf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ibf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ibf RCSB], [http://www.ebi.ac.uk/pdbsum/1ibf 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=1ibf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ibf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ibf RCSB], [http://www.ebi.ac.uk/pdbsum/1ibf PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SODC_PHOLE SODC_PHOLE]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Photobacterium leiognathi]]		[[Category: Photobacterium leiognathi]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]
-	[[Category: Battistoni, A.]]	+	[[Category: Battistoni, A]]
-	[[Category: Bolognesi, M.]]	+	[[Category: Bolognesi, M]]
-	[[Category: Bordo, D.]]	+	[[Category: Bordo, D]]
-	[[Category: Desideri, A.]]	+	[[Category: Desideri, A]]
-	[[Category: Milani, M.]]	+	[[Category: Milani, M]]
-	[[Category: Neill, P O.]]	+	[[Category: Neill, P O]]
-	[[Category: Orazio, M D.]]	+	[[Category: Orazio, M D]]
-	[[Category: Pesce, A.]]	+	[[Category: Pesce, A]]
-	[[Category: Rosano, C.]]	+	[[Category: Rosano, C]]
-	[[Category: Stroppolo, M E.]]	+	[[Category: Stroppolo, M E]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Prokaryotic superoxide dismutase]]		[[Category: Prokaryotic superoxide dismutase]]
	[[Category: Subunit interaction]]		[[Category: Subunit interaction]]

OCA at 09:38, 28 September 2014

OCA — Sun, 28 Sep 2014 09:38:14 GMT

←Older revision		Revision as of 09:38, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1ibf.~~png~~\|~~left~~\|200px]]	+	==X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT V29G==
		+	<StructureSection load='1ibf' size='340' side='right' caption='[[1ibf]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ibf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Photobacterium_leiognathi Photobacterium leiognathi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IBF FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bzo\|1bzo]], [[1ib5\|1ib5]], [[1ibb\|1ibb]], [[1ibd\|1ibd]], [[1ibh\|1ibh]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </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=1ibf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ibf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ibf RCSB], [http://www.ebi.ac.uk/pdbsum/1ibf 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/ib/1ibf_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 ==
		+	The functional properties and X-ray structures of five mutant forms of Photobacterium leiognathi Cu,Zn superoxide dismutase carrying single mutations at residues located at the dimer association interface have been investigated. When compared to the wild-type enzyme, the three-dimensional structures of the mutants show structural perturbations limited to the proximity of the mutation sites and substantial identity of active site geometry. Nonetheless, the catalytic rates of all mutants, measured at neutral pH and low ionic strength by pulse radiolysis, are higher than that of the wild-type protein. Such enzymatic activity increase is paralleled by enhanced active site accessibility to external chelating agents, which, in the mutated enzyme, remove more readily the active site copper ion. It is concluded that mutations at the prokaryotic Cu,Zn superoxide dismutase subunit interface can transduce dynamical perturbation to the active site region, promoting substrate active site accessibility. Such long-range intramolecular communication effects have not been extensively described before within the Cu,Zn superoxide dismutase homology family.

-	~~{{STRUCTURE_1ibf\| PDB=1ibf \| SCENE= }}~~	+	Single mutations at the subunit interface modulate copper reactivity in Photobacterium leiognathi Cu,Zn superoxide dismutase.,Stroppolo ME, Pesce A, D'Orazio M, O'Neill P, Bordo D, Rosano C, Milani M, Battistoni A, Bolognesi M, Desideri A J Mol Biol. 2001 May 4;308(3):555-63. PMID:11327787<ref>PMID:11327787</ref>

-	~~===X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU~~,~~ZN SOD MUTANT V29G===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11327787}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1ibf]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Photobacterium_leiognathi Photobacterium leiognathi]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1IBF OCA].~~	+

	==See Also==		==See Also==
	*[[Superoxide Dismutase\|Superoxide Dismutase]]		*[[Superoxide Dismutase\|Superoxide Dismutase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:011327787<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Photobacterium leiognathi]]		[[Category: Photobacterium leiognathi]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]

OCA at 12:10, 20 October 2012

OCA — Sat, 20 Oct 2012 12:10:56 GMT

←Older revision		Revision as of 12:10, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1ibf]] is a 1 chain structure ~~of [[Superoxide Dismutase]]~~ with sequence from [http://en.wikipedia.org/wiki/Photobacterium_leiognathi Photobacterium leiognathi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBF OCA].	+	[[1ibf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Photobacterium_leiognathi Photobacterium leiognathi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBF OCA].

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

OCA at 07:52, 26 July 2012

OCA — Thu, 26 Jul 2012 07:52:38 GMT

←Older revision		Revision as of 07:52, 26 July 2012
Line 1:		Line 1:
	[[Image:1ibf.png\|left\|200px]]		[[Image:1ibf.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1ibf", 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_1ibf\| PDB=1ibf \| SCENE= }}		{{STRUCTURE_1ibf\| PDB=1ibf \| SCENE= }}

	===X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT V29G===		===X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT V29G===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11327787}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11327787 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_11327787}}		{{ABSTRACT_PUBMED_11327787}}

Line 22:		Line 11:

	==See Also==		==See Also==
-	*[[Superoxide Dismutase]]	+	*[[Superoxide Dismutase\|Superoxide Dismutase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11327787~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011327787</ref><references group="xtra"/>
	[[Category: Photobacterium leiognathi]]		[[Category: Photobacterium leiognathi]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]