5mwk - Revision history

OCA at 17:52, 8 November 2023

OCA — Wed, 08 Nov 2023 17:52:17 GMT

←Older revision		Revision as of 17:52, 8 November 2023
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	<StructureSection load='5mwk' size='340' side='right'caption='[[5mwk]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5mwk' size='340' side='right'caption='[[5mwk]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mwk]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_thetaiotaomicron"_distaso_1912 "bacillus~~ thetaiotaomicron~~" distaso 1912~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MWK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5MWK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mwk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MWK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MWK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=~~ARA~~:ALPHA-L-~~ARABINOSE~~'>~~ARA~~</scene>, <scene name='pdbligand=BR:~~BROMIDE~~+~~ION~~'>BR</scene>, <scene name='pdbligand=CA:~~CALCIUM+ION~~'>CA</scene>, <scene name='pdbligand=~~IOD~~:~~IODIDE~~+ION'>~~IOD~~</scene>, <scene name='pdbligand=~~GAL~~:~~BETA-D-GALACTOSE~~'>~~GAL~~</scene>, <scene name='pdbligand=~~RAM~~:~~ALPHA~~-L-~~RHAMNOSE~~'>~~RAM~~</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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~8OQ~~:~~ALPHA-D-ACERIC~~+~~ACID~~'>~~8OQ~~</scene>, <scene name='pdbligand=~~8PK~~:~~2-O-METHYL,+4-O-ACETYL-~~ALPHA-L-~~FUCOSEPYRANOSE~~'>~~8PK~~</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8OQ:ALPHA-D-ACERIC+ACID'>8OQ</scene>, <scene name='pdbligand=8PK:2-O-METHYL,+4-O-ACETYL-ALPHA-L-FUCOSEPYRANOSE'>8PK</scene>, <scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_0986 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=818 "Bacillus thetaiotaomicron" Distaso 1912])</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=5mwk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mwk OCA], [https://pdbe.org/5mwk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mwk RCSB], [https://www.ebi.ac.uk/pdbsum/5mwk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mwk ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5mwk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mwk OCA], [~~http~~://pdbe.org/5mwk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5mwk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5mwk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5mwk ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8A931_BACTN Q8A931_BACTN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ thetaiotaomicron ~~distaso 1912~~]]	+	[[Category: Bacteroides thetaiotaomicron]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Basle, A]]	+	[[Category: Basle A]]
-	[[Category: Cartmell, A]]	+	[[Category: Cartmell A]]
-	[[Category: Gilbert~~, H J~~]]	+	[[Category: Gilbert HJ]]
-	[[Category: Labourel, A]]	+	[[Category: Labourel A]]
-	[[Category: Luis~~, A S~~]]	+	[[Category: Luis AS]]
-	[[Category: Ndeh, D]]	+	[[Category: Ndeh D]]
-	[[Category: Rogowski, A]]	+	[[Category: Rogowski A]]
-	[[Category: Venditto, I]]	+	[[Category: Venditto I]]
-	~~[[Category: Cazy family 106]]~~	+
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Plant pectin]]~~	+
-	~~[[Category: Rhamnosidase~~]]	+

OCA at 07:31, 19 August 2020

OCA — Wed, 19 Aug 2020 07:31:02 GMT

←Older revision		Revision as of 07:31, 19 August 2020
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	==Glycoside hydrolase BT_0986==		==Glycoside hydrolase BT_0986==
-	<StructureSection load='5mwk' size='340' side='right' caption='[[5mwk]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5mwk' size='340' side='right'caption='[[5mwk]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mwk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MWK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5MWK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mwk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_thetaiotaomicron"_distaso_1912 "bacillus thetaiotaomicron" distaso 1912]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MWK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5MWK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~8OQ~~:ALPHA-D-~~ACERIC+ACID~~'>~~8OQ~~</scene>, <scene name='pdbligand=~~8PK~~:~~2-O-METHYL,~~+~~4-O-ACETYL-ALPHA-L-FUCOSEPYRANOSE~~'>~~8PK~~</scene>, <scene name='pdbligand=~~ARA~~:~~ALPHA-L-ARABINOSE~~'>~~ARA~~</scene>, <scene name='pdbligand=BR:~~BROMIDE~~+ION'>BR</scene>, <scene name='pdbligand=CA:~~CALCIUM+ION~~'>CA</scene>, <scene name='pdbligand=~~GAL~~:~~BETA~~-D-~~GALACTOSE~~'>~~GAL~~</scene>, <scene name='pdbligand=~~IOD~~:~~IODIDE~~+~~ION~~'>~~IOD~~</scene>, <scene name='pdbligand=~~RAM~~:ALPHA-L-~~RHAMNOSE~~'>~~RAM~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</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=5mwk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mwk OCA], [http://pdbe.org/5mwk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mwk RCSB], [http://www.ebi.ac.uk/pdbsum/5mwk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mwk ProSAT]</span></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OQ:ALPHA-D-ACERIC+ACID'>8OQ</scene>, <scene name='pdbligand=8PK:2-O-METHYL,+4-O-ACETYL-ALPHA-L-FUCOSEPYRANOSE'>8PK</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_0986 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=818 "Bacillus thetaiotaomicron" Distaso 1912])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5mwk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mwk OCA], [http://pdbe.org/5mwk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mwk RCSB], [http://www.ebi.ac.uk/pdbsum/5mwk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mwk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus thetaiotaomicron distaso 1912]]
		+	[[Category: Large Structures]]
	[[Category: Basle, A]]		[[Category: Basle, A]]
	[[Category: Cartmell, A]]		[[Category: Cartmell, A]]

OCA at 06:49, 5 April 2017

OCA — Wed, 05 Apr 2017 06:49:32 GMT

←Older revision		Revision as of 06:49, 5 April 2017
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	<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=5mwk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mwk OCA], [http://pdbe.org/5mwk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mwk RCSB], [http://www.ebi.ac.uk/pdbsum/5mwk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mwk 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=5mwk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mwk OCA], [http://pdbe.org/5mwk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mwk RCSB], [http://www.ebi.ac.uk/pdbsum/5mwk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mwk ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The metabolism of carbohydrate polymers drives microbial diversity in the human gut microbiota. It is unclear, however, whether bacterial consortia or single organisms are required to depolymerize highly complex glycans. Here we show that the gut bacterium Bacteroides thetaiotaomicron uses the most structurally complex glycan known: the plant pectic polysaccharide rhamnogalacturonan-II, cleaving all but 1 of its 21 distinct glycosidic linkages. The deconstruction of rhamnogalacturonan-II side chains and backbone are coordinated to overcome steric constraints, and the degradation involves previously undiscovered enzyme families and catalytic activities. The degradation system informs revision of the current structural model of rhamnogalacturonan-II and highlights how individual gut bacteria orchestrate manifold enzymes to metabolize the most challenging glycan in the human diet.
		+
		+	Complex pectin metabolism by gut bacteria reveals novel catalytic functions.,Ndeh D, Rogowski A, Cartmell A, Luis AS, Basle A, Gray J, Venditto I, Briggs J, Zhang X, Labourel A, Terrapon N, Buffetto F, Nepogodiev S, Xiao Y, Field RA, Zhu Y, O'Neill MA, Urbanowicz BR, York WS, Davies GJ, Abbott DW, Ralet MC, Martens EC, Henrissat B, Gilbert HJ Nature. 2017 Mar 22. doi: 10.1038/nature21725. PMID:28329766<ref>PMID:28329766</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5mwk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:24, 22 March 2017

OCA — Wed, 22 Mar 2017 16:24:44 GMT

←Older revision		Revision as of 16:24, 22 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5mwk ~~is ON HOLD until Paper Publication~~	+	==Glycoside hydrolase BT_0986==
-		+	<StructureSection load='5mwk' size='340' side='right' caption='[[5mwk]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors~~: ~~Basle, A~~.~~, Ndeh, D~~.~~, Rogowski, A~~.~~, Cartmell, A~~.~~, Luis, A~~.S., ~~Venditto~~, I., ~~Labourel~~, A., ~~Gilbert~~, ~~H.J.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5mwk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MWK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MWK FirstGlance]. <br>
-	~~Description~~: ~~Glycoside hydrolase BT_0986~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OQ:ALPHA-D-ACERIC+ACID'>8OQ</scene>, <scene name='pdbligand=8PK:2-O-METHYL,+4-O-ACETYL-ALPHA-L-FUCOSEPYRANOSE'>8PK</scene>, <scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures]~~]	+	<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=5mwk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mwk OCA], [http://pdbe.org/5mwk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mwk RCSB], [http://www.ebi.ac.uk/pdbsum/5mwk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mwk ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Luis~~, A.S]]	+	</table>
-	[~~[Category~~: ~~Ndeh~~, D]]	+	__TOC__
-	[[Category: ~~Venditto~~, I]]	+	</StructureSection>
		+	[[Category: Basle, A]]
	[[Category: Cartmell, A]]		[[Category: Cartmell, A]]
		+	[[Category: Gilbert, H J]]
	[[Category: Labourel, A]]		[[Category: Labourel, A]]
-	[[Category: ~~Basle~~, A]]	+	[[Category: Luis, A S]]
-	[[Category: ~~Gilbert~~, ~~H.J~~]]	+	[[Category: Ndeh, D]]
	[[Category: Rogowski, A]]		[[Category: Rogowski, A]]
		+	[[Category: Venditto, I]]
		+	[[Category: Cazy family 106]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Plant pectin]]
		+	[[Category: Rhamnosidase]]

OCA at 11:43, 9 March 2017

OCA — Thu, 09 Mar 2017 11:43:40 GMT

←Older revision		Revision as of 11:43, 9 March 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5mwk is ON HOLD	+	The entry 5mwk is ON HOLD until Paper Publication

	Authors: Basle, A., Ndeh, D., Rogowski, A., Cartmell, A., Luis, A.S., Venditto, I., Labourel, A., Gilbert, H.J.		Authors: Basle, A., Ndeh, D., Rogowski, A., Cartmell, A., Luis, A.S., Venditto, I., Labourel, A., Gilbert, H.J.
Line 7:		Line 7:
	Description: Glycoside hydrolase BT_0986		Description: Glycoside hydrolase BT_0986
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Cartmell, A]]
-	[[Category: Labourel, A]]
-	[[Category: Gilbert, H.J]]
	[[Category: Luis, A.S]]		[[Category: Luis, A.S]]
	[[Category: Ndeh, D]]		[[Category: Ndeh, D]]
	[[Category: Venditto, I]]		[[Category: Venditto, I]]
		+	[[Category: Cartmell, A]]
		+	[[Category: Labourel, A]]
	[[Category: Basle, A]]		[[Category: Basle, A]]
		+	[[Category: Gilbert, H.J]]
	[[Category: Rogowski, A]]		[[Category: Rogowski, A]]

OCA: Protected "5mwk" [edit=sysop:move=sysop]

OCA — Wed, 25 Jan 2017 20:41:00 GMT

Protected "5mwk" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:41, 25 January 2017

OCA: New page: '''Unreleased structure''' The entry 5mwk is ON HOLD Authors: Basle, A., Ndeh, D., Rogowski, A., Cartmell, A., Luis, A.S., Venditto, I., Labourel, A., Gilbert, H.J. Description: Glycos...

OCA — Wed, 25 Jan 2017 20:40:58 GMT

New page: '''Unreleased structure''' The entry 5mwk is ON HOLD Authors: Basle, A., Ndeh, D., Rogowski, A., Cartmell, A., Luis, A.S., Venditto, I., Labourel, A., Gilbert, H.J. Description: Glycos...

New page

'''Unreleased structure'''

The entry 5mwk is ON HOLD

Authors: Basle, A., Ndeh, D., Rogowski, A., Cartmell, A., Luis, A.S., Venditto, I., Labourel, A., Gilbert, H.J.

Description: Glycoside hydrolase BT_0986
[[Category: Unreleased Structures]]
[[Category: Cartmell, A]]
[[Category: Labourel, A]]
[[Category: Gilbert, H.J]]
[[Category: Luis, A.S]]
[[Category: Ndeh, D]]
[[Category: Venditto, I]]
[[Category: Basle, A]]
[[Category: Rogowski, A]]