1ee6 - Revision history

OCA at 10:01, 20 March 2024

2024-03-20T10:01:27Z

←Older revision		Revision as of 10:01, 20 March 2024
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	<StructureSection load='1ee6' size='340' side='right'caption='[[1ee6]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1ee6' size='340' side='right'caption='[[1ee6]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ee6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EE6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EE6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ee6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._KSM-P15 Bacillus sp. KSM-P15]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EE6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EE6 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>~~</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]] 2.3Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https://en.wikipedia.org/wiki/Pectate_lyase Pectate lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.2 4.2.2.2]~~ </~~span~~></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></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=1ee6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ee6 OCA], [https://pdbe.org/1ee6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ee6 RCSB], [https://www.ebi.ac.uk/pdbsum/1ee6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ee6 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=1ee6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ee6 OCA], [https://pdbe.org/1ee6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ee6 RCSB], [https://www.ebi.ac.uk/pdbsum/1ee6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ee6 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9RHW0_BACSP Q9RHW0_BACSP]
	== 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=1ee6 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=1ee6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The crystal structure of a highly alkaline low molecular weight pectate lyase (Pel-15) was determined at 1.5 A resolution by the multiple isomorphous replacement (MIR) method. This is the first pectate lyase structure from polysaccharide lyase family 3. The overall structure is a simple eight-turn right-handed parallel beta-helix domain with one long loop protruding from one side of the beta-helix. The low molecular weight of Pel-15 derives from the lack of N- and C-terminal extensions that are found in many beta-helix proteins. Although the structure has one calcium ion at pH 6.7, raising the pH to 9.5 results in the binding of an additional calcium ion. The common calcium ion found in both the pH 6.5 and 9.5 structures seems to stabilize both the beta-helix structure and the long protruding loop. The additional calcium ion found in the pH 9.5 structure alone may neutralize the acidic substrate. The region around the additional calcium ion is thought to bind to the substrate, as this region is rich in charged amino-acid residues which are required in catalysis.
-
-	The first structure of pectate lyase belonging to polysaccharide lyase family 3.,Akita M, Suzuki A, Kobayashi T, Ito S, Yamane T Acta Crystallogr D Biol Crystallogr. 2001 Dec;57(Pt 12):1786-92. Epub 2001, Nov 21. PMID:11717490<ref>PMID:11717490</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ee6" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus sp]]	+	[[Category: Bacillus sp. KSM-P15]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Pectate lyase]]~~	+	[[Category: Akita M]]
-	[[Category: Akita, M]]	+	[[Category: Ito S]]
-	[[Category: Ito, S]]	+	[[Category: Kobayashi T]]
-	[[Category: Kobayashi, T]]	+	[[Category: Suzuki A]]
-	[[Category: Suzuki, A]]	+	[[Category: Yamane T]]
-	[[Category: Yamane, T]]	+
-	~~[[Category: High-alkaline]]~~	+
-	~~[[Category: Low-molecular-weight]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Parallel beta-helix~~]]	+

OCA at 07:10, 17 March 2021

2021-03-17T07:10:28Z

←Older revision		Revision as of 07:10, 17 March 2021
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	<StructureSection load='1ee6' size='340' side='right'caption='[[1ee6]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1ee6' size='340' side='right'caption='[[1ee6]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ee6]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EE6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1EE6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ee6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EE6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EE6 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></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></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Pectate_lyase Pectate lyase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.2 4.2.2.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pectate_lyase Pectate lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.2 4.2.2.2] </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=1ee6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ee6 OCA], [~~http~~://pdbe.org/1ee6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ee6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ee6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ee6 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=1ee6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ee6 OCA], [https://pdbe.org/1ee6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ee6 RCSB], [https://www.ebi.ac.uk/pdbsum/1ee6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ee6 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 07:20, 12 June 2019

2019-06-12T07:20:40Z

←Older revision		Revision as of 07:20, 12 June 2019
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	==CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15.==		==CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15.==
-	<StructureSection load='1ee6' size='340' side='right' caption='[[1ee6]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='1ee6' size='340' side='right'caption='[[1ee6]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ee6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EE6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EE6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ee6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EE6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EE6 FirstGlance]. <br>
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ee/1ee6_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ee/1ee6_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 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus sp]]		[[Category: Bacillus sp]]
		+	[[Category: Large Structures]]
	[[Category: Pectate lyase]]		[[Category: Pectate lyase]]
	[[Category: Akita, M]]		[[Category: Akita, M]]

OCA at 04:00, 6 September 2017

2017-09-06T04:00:38Z

←Older revision		Revision as of 04:00, 6 September 2017
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		+
	==CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15.==		==CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15.==
	<StructureSection load='1ee6' size='340' side='right' caption='[[1ee6]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1ee6' size='340' side='right' caption='[[1ee6]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ee6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp.~~_ksm-p15~~ Bacillus sp. ~~ksm-p15~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EE6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EE6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ee6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EE6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EE6 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></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></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pectate_lyase Pectate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.2 4.2.2.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pectate_lyase Pectate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.2 4.2.2.2] </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=1ee6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ee6 OCA], [http://pdbe.org/1ee6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ee6 RCSB], [http://www.ebi.ac.uk/pdbsum/1ee6 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=1ee6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ee6 OCA], [http://pdbe.org/1ee6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ee6 RCSB], [http://www.ebi.ac.uk/pdbsum/1ee6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ee6 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<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=1ee6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus sp~~. ksm-p15~~]]	+	[[Category: Bacillus sp]]
	[[Category: Pectate lyase]]		[[Category: Pectate lyase]]
	[[Category: Akita, M]]		[[Category: Akita, M]]

OCA at 12:34, 11 September 2015

2015-09-11T12:34:32Z

←Older revision		Revision as of 12:34, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1ee6' size='340' side='right' caption='[[1ee6]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1ee6' size='340' side='right' caption='[[1ee6]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ee6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EE6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EE6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ee6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp._ksm-p15 Bacillus sp. ksm-p15]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EE6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EE6 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></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></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pectate_lyase Pectate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.2 4.2.2.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pectate_lyase Pectate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.2 4.2.2.2] </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=1ee6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ee6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ee6 RCSB], [http://www.ebi.ac.uk/pdbsum/1ee6 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=1ee6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ee6 OCA], [http://pdbe.org/1ee6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ee6 RCSB], [http://www.ebi.ac.uk/pdbsum/1ee6 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 1ee6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus sp]]	+	[[Category: Bacillus sp. ksm-p15]]
	[[Category: Pectate lyase]]		[[Category: Pectate lyase]]
	[[Category: Akita, M]]		[[Category: Akita, M]]

OCA at 20:49, 22 December 2014

2014-12-22T20:49:58Z

←Older revision		Revision as of 20:49, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ee6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EE6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EE6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ee6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EE6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EE6 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pectate_lyase Pectate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.2 4.2.2.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pectate_lyase Pectate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.2 4.2.2.2] </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=1ee6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ee6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ee6 RCSB], [http://www.ebi.ac.uk/pdbsum/1ee6 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=1ee6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ee6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ee6 RCSB], [http://www.ebi.ac.uk/pdbsum/1ee6 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: Bacillus sp.]]	+	[[Category: Bacillus sp]]
	[[Category: Pectate lyase]]		[[Category: Pectate lyase]]
-	[[Category: Akita, M.]]	+	[[Category: Akita, M]]
-	[[Category: Ito, S.]]	+	[[Category: Ito, S]]
-	[[Category: Kobayashi, T.]]	+	[[Category: Kobayashi, T]]
-	[[Category: Suzuki, A.]]	+	[[Category: Suzuki, A]]
-	[[Category: Yamane, T.]]	+	[[Category: Yamane, T]]
	[[Category: High-alkaline]]		[[Category: High-alkaline]]
	[[Category: Low-molecular-weight]]		[[Category: Low-molecular-weight]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Parallel beta-helix]]		[[Category: Parallel beta-helix]]

OCA at 11:30, 24 September 2014

2014-09-24T11:30:56Z

←Older revision		Revision as of 11:30, 24 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1ee6.~~png\|left~~\|200px]]	+	==CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15.==
		+	<StructureSection load='1ee6' size='340' side='right' caption='[[1ee6]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ee6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EE6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EE6 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pectate_lyase Pectate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.2 4.2.2.2] </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=1ee6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ee6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ee6 RCSB], [http://www.ebi.ac.uk/pdbsum/1ee6 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/ee/1ee6_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 crystal structure of a highly alkaline low molecular weight pectate lyase (Pel-15) was determined at 1.5 A resolution by the multiple isomorphous replacement (MIR) method. This is the first pectate lyase structure from polysaccharide lyase family 3. The overall structure is a simple eight-turn right-handed parallel beta-helix domain with one long loop protruding from one side of the beta-helix. The low molecular weight of Pel-15 derives from the lack of N- and C-terminal extensions that are found in many beta-helix proteins. Although the structure has one calcium ion at pH 6.7, raising the pH to 9.5 results in the binding of an additional calcium ion. The common calcium ion found in both the pH 6.5 and 9.5 structures seems to stabilize both the beta-helix structure and the long protruding loop. The additional calcium ion found in the pH 9.5 structure alone may neutralize the acidic substrate. The region around the additional calcium ion is thought to bind to the substrate, as this region is rich in charged amino-acid residues which are required in catalysis.

-	~~{{STRUCTURE_1ee6\| PDB=1ee6 \| SCENE= }}~~	+	The first structure of pectate lyase belonging to polysaccharide lyase family 3.,Akita M, Suzuki A, Kobayashi T, Ito S, Yamane T Acta Crystallogr D Biol Crystallogr. 2001 Dec;57(Pt 12):1786-92. Epub 2001, Nov 21. PMID:11717490<ref>PMID:11717490</ref>

-	~~===CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15.===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~==About this Structure==~~	+	<references/>
-	~~[[1ee6]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_sp~~. ~~Bacillus sp.]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1EE6 OCA].~~	+	__TOC__
-		+	</StructureSection>
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:011717490<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Bacillus sp.]]		[[Category: Bacillus sp.]]
	[[Category: Pectate lyase]]		[[Category: Pectate lyase]]

OCA: Protected "1ee6" [edit=sysop:move=sysop]

2012-11-08T14:42:06Z

Protected "1ee6" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:42, 8 November 2012

OCA at 14:42, 8 November 2012

2012-11-08T14:42:04Z

←Older revision		Revision as of 14:42, 8 November 2012
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-	{{Seed}}
	[[Image:1ee6.png\|left\|200px]]		[[Image:1ee6.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1ee6", 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_1ee6\| PDB=1ee6 \| SCENE= }}		{{STRUCTURE_1ee6\| PDB=1ee6 \| SCENE= }}

	===CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15.===		===CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15.===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11717490}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11717490 is the PubMed ID number.
-	-->
-	{{ABSTRACT_PUBMED_11717490}}

	==About this Structure==		==About this Structure==
-	~~1EE6~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EE6 OCA].	+	[[1ee6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EE6 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11717490~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011717490</ref><references group="xtra"/>
	[[Category: Bacillus sp.]]		[[Category: Bacillus sp.]]
	[[Category: Pectate lyase]]		[[Category: Pectate lyase]]
Line 33:		Line 20:
	[[Category: High-alkaline]]		[[Category: High-alkaline]]
	[[Category: Low-molecular-weight]]		[[Category: Low-molecular-weight]]
		+	[[Category: Lyase]]
	[[Category: Parallel beta-helix]]		[[Category: Parallel beta-helix]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:49:00 2009''

OCA at 19:49, 17 February 2009

2009-02-17T19:49:03Z

←Older revision		Revision as of 19:49, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1EE6 is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EE6 OCA].	+	1EE6 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EE6 OCA].

	==Reference==		==Reference==
-	The first structure of pectate lyase belonging to polysaccharide lyase family 3., Akita M, Suzuki A, Kobayashi T, Ito S, Yamane T, Acta Crystallogr D Biol Crystallogr. 2001 Dec;57(Pt 12):1786-92. Epub 2001, Nov 21. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/11717490 11717490]~~	+	<ref group="xtra">PMID:11717490</ref><references group="xtra"/>
	[[Category: Bacillus sp.]]		[[Category: Bacillus sp.]]
	[[Category: Pectate lyase]]		[[Category: Pectate lyase]]
-	[[Category: Single protein]]
	[[Category: Akita, M.]]		[[Category: Akita, M.]]
	[[Category: Ito, S.]]		[[Category: Ito, S.]]
Line 36:		Line 35:
	[[Category: Parallel beta-helix]]		[[Category: Parallel beta-helix]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 1 00~~:33:~~38 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:49:00 2009''