5muj - Revision history

OCA at 17:50, 8 November 2023

OCA — Wed, 08 Nov 2023 17:50:27 GMT

←Older revision		Revision as of 17:50, 8 November 2023
Line 3:		Line 3:
	<StructureSection load='5muj' size='340' side='right'caption='[[5muj]], [[Resolution\|resolution]] 1.37Å' scene=''>		<StructureSection load='5muj' size='340' side='right'caption='[[5muj]], [[Resolution\|resolution]] 1.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5muj]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bactn Bactn~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MUJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5MUJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5muj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_VPI-5482 Bacteroides thetaiotaomicron VPI-5482]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MUJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MUJ 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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene>, <scene name='pdbligand=XXM:(2S,3R,4R)-4-(HYDROXYMETHYL)OXOLANE-2,3,4-TRIOL'>XXM</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]] 1.37Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene>, <scene name='pdbligand=XXM:(2S,3R,4R)-4-(HYDROXYMETHYL)OXOLANE-2,3,4-TRIOL'>XXM</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_0996 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 BACTN])~~</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=5muj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5muj OCA], [https://pdbe.org/5muj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5muj RCSB], [https://www.ebi.ac.uk/pdbsum/5muj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5muj 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=5muj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5muj OCA], [~~http~~://pdbe.org/5muj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5muj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5muj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5muj ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8A921_BACTN Q8A921_BACTN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bactn~~]]	+	[[Category: Bacteroides thetaiotaomicron VPI-5482]]
	[[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: Arabinofuranosidase]]~~	+
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Plant pectin]]~~	+
-	~~[[Category: Rgii~~]]	+

OCA at 06:38, 16 October 2019

OCA — Wed, 16 Oct 2019 06:38:59 GMT

←Older revision		Revision as of 06:38, 16 October 2019
Line 1:		Line 1:

	==BT0996 RGII Chain B Complex==		==BT0996 RGII Chain B Complex==
-	<StructureSection load='5muj' size='340' side='right' caption='[[5muj]], [[Resolution\|resolution]] 1.37Å' scene=''>	+	<StructureSection load='5muj' size='340' side='right'caption='[[5muj]], [[Resolution\|resolution]] 1.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5muj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MUJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MUJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5muj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bactn Bactn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MUJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MUJ 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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene>, <scene name='pdbligand=XXM:(2S,3R,4R)-4-(HYDROXYMETHYL)OXOLANE-2,3,4-TRIOL'>XXM</scene></td></tr>		</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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene>, <scene name='pdbligand=XXM:(2S,3R,4R)-4-(HYDROXYMETHYL)OXOLANE-2,3,4-TRIOL'>XXM</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_0996 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 BACTN])</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=5muj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5muj OCA], [http://pdbe.org/5muj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5muj RCSB], [http://www.ebi.ac.uk/pdbsum/5muj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5muj 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=5muj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5muj OCA], [http://pdbe.org/5muj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5muj RCSB], [http://www.ebi.ac.uk/pdbsum/5muj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5muj ProSAT]</span></td></tr>
	</table>		</table>
Line 17:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5muj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5muj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Galactosidase 3D structures\|Galactosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bactn]]
		+	[[Category: Large Structures]]
	[[Category: Basle, A]]		[[Category: Basle, A]]
	[[Category: Cartmell, A]]		[[Category: Cartmell, A]]

OCA at 13:23, 5 April 2017

OCA — Wed, 05 Apr 2017 13:23:17 GMT

←Older revision		Revision as of 13:23, 5 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5muj is ~~ON HOLD~~	+	==BT0996 RGII Chain B Complex==
		+	<StructureSection load='5muj' size='340' side='right' caption='[[5muj]], [[Resolution\|resolution]] 1.37Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5muj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MUJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MUJ 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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ARA:ALPHA-L-ARABINOSE'>ARA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene>, <scene name='pdbligand=XXM:(2S,3R,4R)-4-(HYDROXYMETHYL)OXOLANE-2,3,4-TRIOL'>XXM</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=5muj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5muj OCA], [http://pdbe.org/5muj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5muj RCSB], [http://www.ebi.ac.uk/pdbsum/5muj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5muj ProSAT]</span></td></tr>
		+	</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.

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

-	~~Description: BT0996 RGII Chain B Complex~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category: Luis~~, A.S]]	+	<div class="pdbe-citations 5muj" style="background-color:#fffaf0;"></div>
-	~~[[Category~~: ~~Ndeh, D]]~~	+	== References ==
-	[[Category: ~~Venditto~~, I]]	+	<references/>
		+	__TOC__
		+	</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: Arabinofuranosidase]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Plant pectin]]
		+	[[Category: Rgii]]

OCA at 11:40, 9 March 2017

OCA — Thu, 09 Mar 2017 11:40:14 GMT

←Older revision		Revision as of 11:40, 9 March 2017
Line 7:		Line 7:
	Description: BT0996 RGII Chain B Complex		Description: BT0996 RGII Chain B Complex
	[[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 "5muj" [edit=sysop:move=sysop]

OCA — Wed, 25 Jan 2017 20:35:17 GMT

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

←Older revision

Revision as of 20:35, 25 January 2017

OCA: New page: '''Unreleased structure''' The entry 5muj is ON HOLD Authors: Cartmell, A., Basle, A., Ndeh, D., Luis, A.S., Venditto, I., Labourel, A., Rogowski, A., Gilbert, H.J. Description: BT0996...

OCA — Wed, 25 Jan 2017 20:35:16 GMT

New page: '''Unreleased structure''' The entry 5muj is ON HOLD Authors: Cartmell, A., Basle, A., Ndeh, D., Luis, A.S., Venditto, I., Labourel, A., Rogowski, A., Gilbert, H.J. Description: BT0996...

New page

'''Unreleased structure'''

The entry 5muj is ON HOLD

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

Description: BT0996 RGII Chain B Complex
[[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]]