1y3p - Revision history

OCA at 08:10, 25 October 2023

OCA — Wed, 25 Oct 2023 08:10:09 GMT

←Older revision		Revision as of 08:10, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='1y3p' size='340' side='right'caption='[[1y3p]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1y3p' size='340' side='right'caption='[[1y3p]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1y3p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_sp.~~_a1~~ Sphingomonas sp. a1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y3P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1y3p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_sp._A1 Sphingomonas sp. A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y3P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:~~CALCIUM~~+~~ION~~'>CA</scene>, <scene name='pdbligand=~~BEM~~:~~BETA-D-MANNURONIC~~+~~ACID~~'>~~BEM~~</scene>, <scene name='pdbligand=LGU:ALPHA-L-GULURONATE'>LGU</scene>, <scene name='pdbligand=MAV:ALPHA-D-MANNOPYRANURONIC+ACID'>MAV</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]] 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;'>[[1kwh\|1kwh]], [[1j1n\|1j1n]], [[1y3n\|1y3n]], [[1y3q\|1y3q]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEM:BETA-D-MANNURONIC+ACID'>BEM</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=LGU:ALPHA-L-GULURONATE'>LGU</scene>, <scene name='pdbligand=MAV:ALPHA-D-MANNOPYRANURONIC+ACID'>MAV</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=1y3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y3p OCA], [https://pdbe.org/1y3p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y3p RCSB], [https://www.ebi.ac.uk/pdbsum/1y3p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y3p 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=1y3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y3p OCA], [https://pdbe.org/1y3p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y3p RCSB], [https://www.ebi.ac.uk/pdbsum/1y3p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y3p ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9KWT6_SPHSX Q9KWT6_SPHSX]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Sphingomonas sp. a1]]	+	[[Category: Sphingomonas sp. A1]]
-	[[Category: Hashimoto, W]]	+	[[Category: Hashimoto W]]
-	[[Category: Mikami, B]]	+	[[Category: Mikami B]]
-	[[Category: Mishima, Y]]	+	[[Category: Mishima Y]]
-	[[Category: Momma, K]]	+	[[Category: Momma K]]
-	[[Category: Murata, K]]	+	[[Category: Murata K]]
-	~~[[Category: Alginate]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 16:23, 3 November 2021

OCA — Wed, 03 Nov 2021 16:23:26 GMT

←Older revision		Revision as of 16:23, 3 November 2021
Line 3:		Line 3:
	<StructureSection load='1y3p' size='340' side='right'caption='[[1y3p]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1y3p' size='340' side='right'caption='[[1y3p]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1y3p]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Sphingomonas_sp._a1 Sphingomonas sp. a1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1Y3P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1y3p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_sp._a1 Sphingomonas sp. a1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y3P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~BEM~~:~~BETA-D-MANNURONIC~~+~~ACID~~'>~~BEM~~</scene>, <scene name='pdbligand=CA:~~CALCIUM~~+~~ION~~'>CA</scene>, <scene name='pdbligand=LGU:ALPHA-L-GULURONATE'>LGU</scene>, <scene name='pdbligand=MAV:ALPHA-D-MANNOPYRANURONIC+ACID'>MAV</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=BEM:BETA-D-MANNURONIC+ACID'>BEM</scene>, <scene name='pdbligand=LGU:ALPHA-L-GULURONATE'>LGU</scene>, <scene name='pdbligand=MAV:ALPHA-D-MANNOPYRANURONIC+ACID'>MAV</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kwh\|1kwh]], [[1j1n\|1j1n]], [[1y3n\|1y3n]], [[1y3q\|1y3q]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kwh\|1kwh]], [[1j1n\|1j1n]], [[1y3n\|1y3n]], [[1y3q\|1y3q]]</div></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=1y3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y3p OCA], [~~http~~://pdbe.org/1y3p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1y3p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1y3p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1y3p 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=1y3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y3p OCA], [https://pdbe.org/1y3p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y3p RCSB], [https://www.ebi.ac.uk/pdbsum/1y3p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y3p ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 17:24, 29 January 2020

OCA — Wed, 29 Jan 2020 17:24:15 GMT

←Older revision		Revision as of 17:24, 29 January 2020
Line 1:		Line 1:

	==Structure of AlgQ1, alginate-binding protein, complexed with an alginate tetrasaccharide==		==Structure of AlgQ1, alginate-binding protein, complexed with an alginate tetrasaccharide==
-	<StructureSection load='1y3p' size='340' side='right' caption='[[1y3p]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1y3p' size='340' side='right'caption='[[1y3p]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1y3p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sphingomonas_sp._a1 Sphingomonas sp. a1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y3P FirstGlance]. <br>		<table><tr><td colspan='2'>[[1y3p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sphingomonas_sp._a1 Sphingomonas sp. a1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y3P FirstGlance]. <br>
Line 31:		Line 31:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Sphingomonas sp. a1]]		[[Category: Sphingomonas sp. a1]]
	[[Category: Hashimoto, W]]		[[Category: Hashimoto, W]]

OCA at 07:36, 18 April 2018

OCA — Wed, 18 Apr 2018 07:36:32 GMT

←Older revision		Revision as of 07:36, 18 April 2018
Line 1:		Line 1:
		+
	==Structure of AlgQ1, alginate-binding protein, complexed with an alginate tetrasaccharide==		==Structure of AlgQ1, alginate-binding protein, complexed with an alginate tetrasaccharide==
	<StructureSection load='1y3p' size='340' side='right' caption='[[1y3p]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1y3p' size='340' side='right' caption='[[1y3p]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1y3p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sphingomonas_sp._a1 Sphingomonas sp. a1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y3P FirstGlance]. <br>		<table><tr><td colspan='2'>[[1y3p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sphingomonas_sp._a1 Sphingomonas sp. a1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y3P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:~~CALCIUM~~+~~ION~~'>CA</scene>, <scene name='pdbligand=~~BEM~~:~~BETA-D-MANNURONIC~~+~~ACID~~'>~~BEM~~</scene>, <scene name='pdbligand=LGU:ALPHA-L-GULURONATE'>LGU</scene>, <scene name='pdbligand=MAV:ALPHA-D-MANNOPYRANURONIC+ACID'>MAV</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEM:BETA-D-MANNURONIC+ACID'>BEM</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=LGU:ALPHA-L-GULURONATE'>LGU</scene>, <scene name='pdbligand=MAV:ALPHA-D-MANNOPYRANURONIC+ACID'>MAV</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kwh\|1kwh]], [[1j1n\|1j1n]], [[1y3n\|1y3n]], [[1y3q\|1y3q]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kwh\|1kwh]], [[1j1n\|1j1n]], [[1y3n\|1y3n]], [[1y3q\|1y3q]]</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=1y3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y3p OCA], [http://pdbe.org/1y3p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y3p RCSB], [http://www.ebi.ac.uk/pdbsum/1y3p 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=1y3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y3p OCA], [http://pdbe.org/1y3p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y3p RCSB], [http://www.ebi.ac.uk/pdbsum/1y3p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1y3p ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y3/1y3p_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y3/1y3p_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>

OCA at 14:07, 9 February 2016

OCA — Tue, 09 Feb 2016 14:07:45 GMT

←Older revision		Revision as of 14:07, 9 February 2016
Line 15:		Line 15:
	<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=1y3p ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:58, 10 September 2015

OCA — Thu, 10 Sep 2015 22:58:33 GMT

←Older revision		Revision as of 22:58, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1y3p' size='340' side='right' caption='[[1y3p]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1y3p' size='340' side='right' caption='[[1y3p]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1y3p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sphingomonas_sp. Sphingomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y3P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1y3p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sphingomonas_sp._a1 Sphingomonas sp. a1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y3P FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=BEM:BETA-D-MANNURONIC+ACID'>BEM</scene>, <scene name='pdbligand=LGU:ALPHA-L-GULURONATE'>LGU</scene>, <scene name='pdbligand=MAV:ALPHA-D-MANNOPYRANURONIC+ACID'>MAV</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=BEM:BETA-D-MANNURONIC+ACID'>BEM</scene>, <scene name='pdbligand=LGU:ALPHA-L-GULURONATE'>LGU</scene>, <scene name='pdbligand=MAV:ALPHA-D-MANNOPYRANURONIC+ACID'>MAV</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kwh\|1kwh]], [[1j1n\|1j1n]], [[1y3n\|1y3n]], [[1y3q\|1y3q]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kwh\|1kwh]], [[1j1n\|1j1n]], [[1y3n\|1y3n]], [[1y3q\|1y3q]]</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=1y3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y3p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y3p RCSB], [http://www.ebi.ac.uk/pdbsum/1y3p 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=1y3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y3p OCA], [http://pdbe.org/1y3p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y3p RCSB], [http://www.ebi.ac.uk/pdbsum/1y3p PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 1y3p" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Sphingomonas sp]]	+	[[Category: Sphingomonas sp. a1]]
	[[Category: Hashimoto, W]]		[[Category: Hashimoto, W]]
	[[Category: Mikami, B]]		[[Category: Mikami, B]]

OCA at 09:47, 8 January 2015

OCA — Thu, 08 Jan 2015 09:47:36 GMT

←Older revision		Revision as of 09:47, 8 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1y3p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sphingomonas_sp. Sphingomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y3P FirstGlance]. <br>		<table><tr><td colspan='2'>[[1y3p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sphingomonas_sp. Sphingomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y3P FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=BEM:BETA-D-MANNURONIC+ACID'>BEM</scene>, <scene name='pdbligand=LGU:ALPHA-L-GULURONATE'>LGU</scene>, <scene name='pdbligand=MAV:ALPHA-D-MANNOPYRANURONIC+ACID'>MAV</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=BEM:BETA-D-MANNURONIC+ACID'>BEM</scene>, <scene name='pdbligand=LGU:ALPHA-L-GULURONATE'>LGU</scene>, <scene name='pdbligand=MAV:ALPHA-D-MANNOPYRANURONIC+ACID'>MAV</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kwh\|1kwh]], [[1j1n\|1j1n]], [[1y3n\|1y3n]], [[1y3q\|1y3q]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kwh\|1kwh]], [[1j1n\|1j1n]], [[1y3n\|1y3n]], [[1y3q\|1y3q]]</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=1y3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y3p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y3p RCSB], [http://www.ebi.ac.uk/pdbsum/1y3p 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=1y3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y3p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y3p RCSB], [http://www.ebi.ac.uk/pdbsum/1y3p 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 29:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Sphingomonas sp.]]	+	[[Category: Sphingomonas sp]]
-	[[Category: Hashimoto, W.]]	+	[[Category: Hashimoto, W]]
-	[[Category: Mikami, B.]]	+	[[Category: Mikami, B]]
-	[[Category: Mishima, Y.]]	+	[[Category: Mishima, Y]]
-	[[Category: Momma, K.]]	+	[[Category: Momma, K]]
-	[[Category: Murata, K.]]	+	[[Category: Murata, K]]
	[[Category: Alginate]]		[[Category: Alginate]]
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]

OCA at 18:47, 29 September 2014

OCA — Mon, 29 Sep 2014 18:47:03 GMT

←Older revision		Revision as of 18:47, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1y3p.~~png~~\|~~left~~\|200px]]	+	==Structure of AlgQ1, alginate-binding protein, complexed with an alginate tetrasaccharide==
		+	<StructureSection load='1y3p' size='340' side='right' caption='[[1y3p]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1y3p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sphingomonas_sp. Sphingomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y3P FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=BEM:BETA-D-MANNURONIC+ACID'>BEM</scene>, <scene name='pdbligand=LGU:ALPHA-L-GULURONATE'>LGU</scene>, <scene name='pdbligand=MAV:ALPHA-D-MANNOPYRANURONIC+ACID'>MAV</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kwh\|1kwh]], [[1j1n\|1j1n]], [[1y3n\|1y3n]], [[1y3q\|1y3q]]</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=1y3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y3p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y3p RCSB], [http://www.ebi.ac.uk/pdbsum/1y3p 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/y3/1y3p_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 ==
		+	A Gram-negative bacterium, Sphingomonas sp. A1, has a macromolecule (alginate) import system consisting of a pit on the cell surface and an alginate-specific ATP-binding cassette importer in the inner membrane. Transport of alginate from the pit to the ABC importer is probably mediated by two periplasmic binding protein homologues (AlgQ1 and AlgQ2). Here we describe characteristics of binding of AlgQ1 and AlgQ2 to alginate and its oligosaccharides through surface plasmon resonance biosensor analysis, UV absorption difference spectroscopy, and X-ray crystallography. Both AlgQ1 and AlgQ2 were inducibly expressed in the periplasm of alginate-grown cells of strain A1. Biosensor analysis indicated that both proteins specifically bind alginate with a high degree of polymerization (>100) and that dissociation constants for alginate with an average molecular mass of 26 kDa are 2.3 x 10(-)(7) M for AlgQ1 and 1.5 x 10(-)(7) M for AlgQ2. An in vitro ATPase assay using the membrane complex, including the alginate ABC importer, suggested that both alginate-bound forms of AlgQ1 and AlgQ2 are closely associated with the importer. X-ray crystallography showed that AlgQ1 consisted of two domains separated by a deep cleft that binds alginate oligosaccharides through a conformational change in the two domains. These results directly show that alginate-binding proteins play an important role in the efficient transport of alginate macromolecules with different degrees of polymerization in the periplasm.

-	~~{{STRUCTURE_1y3p\| PDB=1y3p \| SCENE= }}~~	+	Direct evidence for Sphingomonas sp. A1 periplasmic proteins as macromolecule-binding proteins associated with the ABC transporter: molecular insights into alginate transport in the periplasm.,Momma K, Mishima Y, Hashimoto W, Mikami B, Murata K Biochemistry. 2005 Apr 5;44(13):5053-64. PMID:15794643<ref>PMID:15794643</ref>

-	~~===Structure of AlgQ1~~, ~~alginate-binding protein, complexed with an alginate tetrasaccharide===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15794643}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1y3p]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Sphingomonas_sp~~. ~~Sphingomonas sp.]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3P OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015794643<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Sphingomonas sp.]]		[[Category: Sphingomonas sp.]]
	[[Category: Hashimoto, W.]]		[[Category: Hashimoto, W.]]

OCA: Protected "1y3p" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 11:32:05 GMT

Protected "1y3p" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:32, 5 January 2013

OCA at 11:32, 5 January 2013

OCA — Sat, 05 Jan 2013 11:32:04 GMT

←Older revision		Revision as of 11:32, 5 January 2013
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-	{{Seed}}
	[[Image:1y3p.png\|left\|200px]]		[[Image:1y3p.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1y3p", 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_1y3p\| PDB=1y3p \| SCENE= }}		{{STRUCTURE_1y3p\| PDB=1y3p \| SCENE= }}

	===Structure of AlgQ1, alginate-binding protein, complexed with an alginate tetrasaccharide===		===Structure of AlgQ1, alginate-binding protein, complexed with an alginate tetrasaccharide===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15794643}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15794643 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15794643}}		{{ABSTRACT_PUBMED_15794643}}

	==About this Structure==		==About this Structure==
-	~~1Y3P~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Sphingomonas_sp. Sphingomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3P OCA].	+	[[1y3p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sphingomonas_sp. Sphingomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3P OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15794643~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015794643</ref><references group="xtra"/>
	[[Category: Sphingomonas sp.]]		[[Category: Sphingomonas sp.]]
	[[Category: Hashimoto, W.]]		[[Category: Hashimoto, W.]]
Line 32:		Line 20:
	[[Category: Alginate]]		[[Category: Alginate]]
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:21:51 2009''