5mdo - Revision history

OCA at 18:40, 1 November 2023

OCA — Wed, 01 Nov 2023 18:40:01 GMT

←Older revision		Revision as of 18:40, 1 November 2023
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	==Crystal structure of in vitro folded Chitoporin VhChip from Vibrio harveyi (crystal form I)==		==Crystal structure of in vitro folded Chitoporin VhChip from Vibrio harveyi (crystal form I)==
-	<StructureSection load='5mdo' size='340' side='right' caption='[[5mdo]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='5mdo' size='340' side='right'caption='[[5mdo]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mdo]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"achromobacter_harveyi"_johnson_and_shunk_1936 "achromobacter~~ harveyi~~" johnson and shunk 1936~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5MDO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mdo]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_harveyi Vibrio harveyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MDO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene~~>, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.95Å</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=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">chiP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=669 "Achromobacter harveyi" Johnson and Shunk 1936])~~</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=5mdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdo OCA], [https://pdbe.org/5mdo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mdo RCSB], [https://www.ebi.ac.uk/pdbsum/5mdo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdo 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=5mdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdo OCA], [~~http~~://pdbe.org/5mdo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5mdo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5mdo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdo ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/L0RVU0_VIBHA L0RVU0_VIBHA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5mdo" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5mdo" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Porin 3D structures\|Porin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Achromobacter harveyi johnson and shunk 1936]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Berg, B van den]]~~	+
-	~~[[Category: Zahn, M]]~~	+
-	~~[[Category: Chitin]]~~	+
-	~~[[Category: Outer membrane protein]]~~	+
-	~~[[Category: Porin]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+
	[[Category: Vibrio harveyi]]		[[Category: Vibrio harveyi]]
		+	[[Category: Zahn M]]
		+	[[Category: Van den Berg B]]

OCA at 20:40, 24 January 2018

OCA — Wed, 24 Jan 2018 20:40:01 GMT

←Older revision		Revision as of 20:40, 24 January 2018
Line 3:		Line 3:
	<StructureSection load='5mdo' size='340' side='right' caption='[[5mdo]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='5mdo' size='340' side='right' caption='[[5mdo]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mdo]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MDO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mdo]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_harveyi"_johnson_and_shunk_1936 "achromobacter harveyi" johnson and shunk 1936]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MDO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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">chiP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=669 "Achromobacter harveyi" Johnson and Shunk 1936])</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=5mdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdo OCA], [http://pdbe.org/5mdo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mdo RCSB], [http://www.ebi.ac.uk/pdbsum/5mdo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdo 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=5mdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdo OCA], [http://pdbe.org/5mdo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mdo RCSB], [http://www.ebi.ac.uk/pdbsum/5mdo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdo ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Chitin, an insoluble polymer of N-acetylglucosamine, is one of the most abundant biopolymers on Earth. By degrading chitin, chitinolytic bacteria such as Vibrio harveyi are critical for chitin recycling and maintenance of carbon and nitrogen cycles in the world's oceans. A decisive step in chitin degradation is the uptake of chito-oligosaccharides by an outer membrane protein channel named chitoporin (ChiP). Here, we report X-ray crystal structures of ChiP from V. harveyi in the presence and absence of chito-oligosaccharides. Structures without bound sugar reveal a trimeric assembly with an unprecedented closing of the transport pore by the N-terminus of a neighboring subunit. Substrate binding ejects the pore plug to open the transport channel. Together with molecular dynamics simulations, electrophysiology and in vitro transport assays our data provide an explanation for the exceptional affinity of ChiP for chito-oligosaccharides and point to an important role of the N-terminal gate in substrate transport.
		+
		+	Structural basis for chitin acquisition by marine Vibrio species.,Aunkham A, Zahn M, Kesireddy A, Pothula KR, Schulte A, Basle A, Kleinekathofer U, Suginta W, van den Berg B Nat Commun. 2018 Jan 15;9(1):220. doi: 10.1038/s41467-017-02523-y. PMID:29335469<ref>PMID:29335469</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5mdo" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Achromobacter harveyi johnson and shunk 1936]]
	[[Category: Berg, B van den]]		[[Category: Berg, B van den]]
	[[Category: Zahn, M]]		[[Category: Zahn, M]]

OCA at 06:07, 20 December 2017

OCA — Wed, 20 Dec 2017 06:07:13 GMT

←Older revision		Revision as of 06:07, 20 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5mdo is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of in vitro folded Chitoporin VhChip from Vibrio harveyi (crystal form I)==
-		+	<StructureSection load='5mdo' size='340' side='right' caption='[[5mdo]], [[Resolution\|resolution]] 1.95Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5mdo]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MDO FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5mdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mdo OCA], [http://pdbe.org/5mdo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mdo RCSB], [http://www.ebi.ac.uk/pdbsum/5mdo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mdo ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Berg, B van den]]
		+	[[Category: Zahn, M]]
		+	[[Category: Chitin]]
		+	[[Category: Outer membrane protein]]
		+	[[Category: Porin]]
		+	[[Category: Sugar binding protein]]
		+	[[Category: Vibrio harveyi]]

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

OCA — Fri, 09 Dec 2016 16:41:15 GMT

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

←Older revision

Revision as of 16:41, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5mdo is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Fri, 09 Dec 2016 16:41:14 GMT

New page: '''Unreleased structure''' The entry 5mdo is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5mdo is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]