1oek - Revision history

OCA at 05:46, 17 April 2024

OCA — Wed, 17 Apr 2024 05:46:50 GMT

←Older revision		Revision as of 05:46, 17 April 2024
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	<StructureSection load='1oek' size='340' side='right'caption='[[1oek]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1oek' size='340' side='right'caption='[[1oek]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1oek]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OEK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OEK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1oek]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OEK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OEK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 2.4Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1oek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oek OCA], [https://pdbe.org/1oek PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oek RCSB], [https://www.ebi.ac.uk/pdbsum/1oek PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oek 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=1oek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oek OCA], [https://pdbe.org/1oek PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oek RCSB], [https://www.ebi.ac.uk/pdbsum/1oek PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oek ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/ZINT_ECOLI ZINT_ECOLI]] May function as a periplasmic zinc chaperone or mediate direct transport of zinc from the periplasm to the cytoplasm under zinc-limited conditions. Binds zinc with high affinity, and can also bind cadmium, mercury or nickel. Preferentially binds Zn(2+) over Cd(2+). Contains one high affinity metal binding site, and can bind additional metal ions at other sites.<ref>PMID:17931600</ref> <ref>PMID:19377097</ref>	+	[https://www.uniprot.org/uniprot/ZINT_ECOLI ZINT_ECOLI] May function as a periplasmic zinc chaperone or mediate direct transport of zinc from the periplasm to the cytoplasm under zinc-limited conditions. Binds zinc with high affinity, and can also bind cadmium, mercury or nickel. Preferentially binds Zn(2+) over Cd(2+). Contains one high affinity metal binding site, and can bind additional metal ions at other sites.<ref>PMID:17931600</ref> <ref>PMID:19377097</ref>
	== 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=1oek 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=1oek ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	We have determined the crystal structure of YodA, an Escherichia coli protein of unknown function. YodA had been identified under conditions of cadmium stress, and we confirm that it binds metals such as cadmium and zinc. We have also found nickel bound in one of the crystal forms. YodA is composed of two domains: a main lipocalin/calycin-like domain and a helical domain. The principal metal-binding site lies on one side of the calycin domain, thus making YodA the first metal-binding lipocalin known. Our experiments suggest that YodA expression may be part of a more general stress response. From sequence analogy with the C-terminal domain of a metal-binding receptor of a member of bacterial ATP-binding cassette transporters, we propose a three-dimensional model for this receptor and suggest that YodA may have a receptor-type partner in E. coli.
-
-	YodA from Escherichia coli is a metal-binding, lipocalin-like protein.,David G, Blondeau K, Schiltz M, Penel S, Lewit-Bentley A J Biol Chem. 2003 Oct 31;278(44):43728-35. Epub 2003 Aug 8. PMID:12909634<ref>PMID:12909634</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1oek" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Blondeau, K]]	+	[[Category: Blondeau K]]
-	[[Category: David, G]]	+	[[Category: David G]]
-	[[Category: Lewit-Bentley, A]]	+	[[Category: Lewit-Bentley A]]
-	[[Category: Penel, S]]	+	[[Category: Penel S]]
-	[[Category: Renouard, M]]	+	[[Category: Renouard M]]
-	~~[[Category: Lipocalin]]~~	+
-	~~[[Category: Metal binding protein]]~~	+
-	~~[[Category: Stress protein]]~~	+
-	~~[[Category: Yoda~~]]	+

OCA at 06:00, 28 April 2021

OCA — Wed, 28 Apr 2021 06:00:44 GMT

←Older revision		Revision as of 06:00, 28 April 2021
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	<StructureSection load='1oek' size='340' side='right'caption='[[1oek]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1oek' size='340' side='right'caption='[[1oek]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1oek]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OEK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1OEK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1oek]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OEK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OEK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></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=1oek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oek OCA], [~~http~~://pdbe.org/1oek PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1oek RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1oek PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1oek 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=1oek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oek OCA], [https://pdbe.org/1oek PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oek RCSB], [https://www.ebi.ac.uk/pdbsum/1oek PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oek ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ZINT_ECOLI ZINT_ECOLI]] May function as a periplasmic zinc chaperone or mediate direct transport of zinc from the periplasm to the cytoplasm under zinc-limited conditions. Binds zinc with high affinity, and can also bind cadmium, mercury or nickel. Preferentially binds Zn(2+) over Cd(2+). Contains one high affinity metal binding site, and can bind additional metal ions at other sites.<ref>PMID:17931600</ref> <ref>PMID:19377097</ref>	+	[[https://www.uniprot.org/uniprot/ZINT_ECOLI ZINT_ECOLI]] May function as a periplasmic zinc chaperone or mediate direct transport of zinc from the periplasm to the cytoplasm under zinc-limited conditions. Binds zinc with high affinity, and can also bind cadmium, mercury or nickel. Preferentially binds Zn(2+) over Cd(2+). Contains one high affinity metal binding site, and can bind additional metal ions at other sites.<ref>PMID:17931600</ref> <ref>PMID:19377097</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:15, 24 July 2019

OCA — Wed, 24 Jul 2019 09:15:04 GMT

←Older revision		Revision as of 09:15, 24 July 2019
Line 1:		Line 1:

	==YodA from Escherichia coli crystallised with zinc ions==		==YodA from Escherichia coli crystallised with zinc ions==
-	<StructureSection load='1oek' size='340' side='right' caption='[[1oek]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='1oek' size='340' side='right'caption='[[1oek]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1oek]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OEK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OEK FirstGlance]. <br>		<table><tr><td colspan='2'>[[1oek]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OEK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OEK FirstGlance]. <br>
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oe/1oek_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oe/1oek_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 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Blondeau, K]]		[[Category: Blondeau, K]]
	[[Category: David, G]]		[[Category: David, G]]

OCA at 07:25, 18 October 2017

OCA — Wed, 18 Oct 2017 07:25:00 GMT

←Older revision		Revision as of 07:25, 18 October 2017
Line 1:		Line 1:
-	==~~YODA FROM ESCHERICHIA COLI CRYSTALLISED WITH ZINC IONS~~==	+
		+	==YodA from Escherichia coli crystallised with zinc ions==
	<StructureSection load='1oek' size='340' side='right' caption='[[1oek]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1oek' size='340' side='right' caption='[[1oek]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1oek]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OEK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OEK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1oek]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OEK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OEK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1oee\|1oee]], [[1oej\|1oej]]</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=1oek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oek OCA], [http://pdbe.org/1oek PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oek RCSB], [http://www.ebi.ac.uk/pdbsum/1oek PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1oek ProSAT]</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=1oek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oek OCA], [http://pdbe.org/1oek PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oek RCSB], [http://www.ebi.ac.uk/pdbsum/1oek PDBsum]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
Line 32:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Blondeau, K]]		[[Category: Blondeau, K]]
	[[Category: David, G]]		[[Category: David, G]]
Line 39:		Line 39:
	[[Category: Renouard, M]]		[[Category: Renouard, M]]
	[[Category: Lipocalin]]		[[Category: Lipocalin]]
		+	[[Category: Metal binding protein]]
	[[Category: Stress protein]]		[[Category: Stress protein]]
-	[[Category: Stress protein-lipocalin complex]]
-	[[Category: Stress protein/lipocalin]]
	[[Category: Yoda]]		[[Category: Yoda]]

OCA at 11:31, 9 February 2016

OCA — Tue, 09 Feb 2016 11:31:00 GMT

←Older revision		Revision as of 11:31, 9 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1oek ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:46, 10 September 2015

OCA — Thu, 10 Sep 2015 21:46:30 GMT

←Older revision		Revision as of 21:46, 10 September 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1oee\|1oee]], [[1oej\|1oej]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1oee\|1oee]], [[1oej\|1oej]]</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=1oek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oek OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1oek RCSB], [http://www.ebi.ac.uk/pdbsum/1oek 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=1oek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oek OCA], [http://pdbe.org/1oek PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oek RCSB], [http://www.ebi.ac.uk/pdbsum/1oek PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~YODA_ECOLI YODA_ECOLI~~]] May function as a periplasmic zinc chaperone or mediate direct transport of zinc from the periplasm to the cytoplasm under zinc-limited conditions. Binds zinc with high affinity, and can also bind cadmium, mercury or nickel. Preferentially binds Zn(2+) over Cd(2+). Contains one high affinity metal binding site, and can bind additional metal ions at other sites.<ref>PMID:17931600</ref> <ref>PMID:19377097</ref>	+	[[http://www.uniprot.org/uniprot/ZINT_ECOLI ZINT_ECOLI]] May function as a periplasmic zinc chaperone or mediate direct transport of zinc from the periplasm to the cytoplasm under zinc-limited conditions. Binds zinc with high affinity, and can also bind cadmium, mercury or nickel. Preferentially binds Zn(2+) over Cd(2+). Contains one high affinity metal binding site, and can bind additional metal ions at other sites.<ref>PMID:17931600</ref> <ref>PMID:19377097</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1oek" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:31, 25 December 2014

OCA — Thu, 25 Dec 2014 06:31:22 GMT

←Older revision		Revision as of 06:31, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1oek]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OEK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OEK FirstGlance]. <br>		<table><tr><td colspan='2'>[[1oek]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OEK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OEK FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1oee\|1oee]], [[1oej\|1oej]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1oee\|1oee]], [[1oej\|1oej]]</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=1oek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oek OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1oek RCSB], [http://www.ebi.ac.uk/pdbsum/1oek 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=1oek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oek OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1oek RCSB], [http://www.ebi.ac.uk/pdbsum/1oek PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/YODA_ECOLI YODA_ECOLI]] May function as a periplasmic zinc chaperone or mediate direct transport of zinc from the periplasm to the cytoplasm under zinc-limited conditions. Binds zinc with high affinity, and can also bind cadmium, mercury or nickel. Preferentially binds Zn(2+) over Cd(2+). Contains one high affinity metal binding site, and can bind additional metal ions at other sites.<ref>PMID:17931600</ref> <ref>PMID:19377097</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Blondeau, K.]]	+	[[Category: Blondeau, K]]
-	[[Category: David, G.]]	+	[[Category: David, G]]
-	[[Category: Lewit-Bentley, A.]]	+	[[Category: Lewit-Bentley, A]]
-	[[Category: Penel, S.]]	+	[[Category: Penel, S]]
-	[[Category: Renouard, M.]]	+	[[Category: Renouard, M]]
	[[Category: Lipocalin]]		[[Category: Lipocalin]]
	[[Category: Stress protein]]		[[Category: Stress protein]]

OCA at 18:03, 28 September 2014

OCA — Sun, 28 Sep 2014 18:03:32 GMT

←Older revision		Revision as of 18:03, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1oek.~~png~~\|~~left~~\|200px]]	+	==YODA FROM ESCHERICHIA COLI CRYSTALLISED WITH ZINC IONS==
		+	<StructureSection load='1oek' size='340' side='right' caption='[[1oek]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1oek]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OEK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OEK FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1oee\|1oee]], [[1oej\|1oej]]</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=1oek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oek OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1oek RCSB], [http://www.ebi.ac.uk/pdbsum/1oek 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/oe/1oek_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 ==
		+	We have determined the crystal structure of YodA, an Escherichia coli protein of unknown function. YodA had been identified under conditions of cadmium stress, and we confirm that it binds metals such as cadmium and zinc. We have also found nickel bound in one of the crystal forms. YodA is composed of two domains: a main lipocalin/calycin-like domain and a helical domain. The principal metal-binding site lies on one side of the calycin domain, thus making YodA the first metal-binding lipocalin known. Our experiments suggest that YodA expression may be part of a more general stress response. From sequence analogy with the C-terminal domain of a metal-binding receptor of a member of bacterial ATP-binding cassette transporters, we propose a three-dimensional model for this receptor and suggest that YodA may have a receptor-type partner in E. coli.

-	~~{{STRUCTURE_1oek\| PDB=1oek \| SCENE= }}~~	+	YodA from Escherichia coli is a metal-binding, lipocalin-like protein.,David G, Blondeau K, Schiltz M, Penel S, Lewit-Bentley A J Biol Chem. 2003 Oct 31;278(44):43728-35. Epub 2003 Aug 8. PMID:12909634<ref>PMID:12909634</ref>

-	~~===YODA FROM ESCHERICHIA COLI CRYSTALLISED WITH ZINC IONS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12909634}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1oek]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1OEK OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012909634<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Blondeau, K.]]		[[Category: Blondeau, K.]]

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

OCA — Wed, 12 Dec 2012 22:09:24 GMT

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

←Older revision

Revision as of 22:09, 12 December 2012

OCA at 22:09, 12 December 2012

OCA — Wed, 12 Dec 2012 22:09:20 GMT

←Older revision		Revision as of 22:09, 12 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1oek.png\|left\|200px]]		[[Image:1oek.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1oek", 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_1oek\| PDB=1oek \| SCENE= }}		{{STRUCTURE_1oek\| PDB=1oek \| SCENE= }}

	===YODA FROM ESCHERICHIA COLI CRYSTALLISED WITH ZINC IONS===		===YODA FROM ESCHERICHIA COLI CRYSTALLISED WITH ZINC IONS===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12909634}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12909634 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12909634}}		{{ABSTRACT_PUBMED_12909634}}

	==About this Structure==		==About this Structure==
-	~~1OEK~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OEK OCA].	+	[[1oek]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OEK OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12909634~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012909634</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Blondeau, K.]]		[[Category: Blondeau, K.]]
Line 32:		Line 20:
	[[Category: Lipocalin]]		[[Category: Lipocalin]]
	[[Category: Stress protein]]		[[Category: Stress protein]]
		+	[[Category: Stress protein-lipocalin complex]]
		+	[[Category: Stress protein/lipocalin]]
	[[Category: Yoda]]		[[Category: Yoda]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 09:25:57 2009''