5x5m - Revision history

OCA at 07:54, 22 November 2023

OCA — Wed, 22 Nov 2023 07:54:14 GMT

←Older revision		Revision as of 07:54, 22 November 2023
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	<StructureSection load='5x5m' size='340' side='right'caption='[[5x5m]], [[Resolution\|resolution]] 1.21Å' scene=''>		<StructureSection load='5x5m' size='340' side='right'caption='[[5x5m]], [[Resolution\|resolution]] 1.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x5m]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5X5M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x5m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Listeria_innocua_Clip11262 Listeria innocua Clip11262]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X5M FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=7YU:(+)~~-~~Yatakemycin'>7YU</scene>~~, ~~<scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</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]] 1.211Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5x5r\|5x5r]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7YU:(+)-Yatakemycin'>7YU</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene></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=5x5m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5m OCA], [~~http~~://pdbe.org/5x5m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x5m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x5m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5m 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=5x5m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5m OCA], [https://pdbe.org/5x5m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x5m RCSB], [https://www.ebi.ac.uk/pdbsum/5x5m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5m ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q929T5_LISIN Q929T5_LISIN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Zhang, J~~]]	+	[[Category: Listeria innocua Clip11262]]
-	[[Category: ~~Hydrolase]]~~	+	[[Category: Zhang J]]
-	~~[[Category: Hydrolase-antibiotic complex~~]]	+

OCA at 07:27, 7 October 2020

OCA — Wed, 07 Oct 2020 07:27:02 GMT

←Older revision		Revision as of 07:27, 7 October 2020
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	==Crystal structure of a hydrolase encoded by lin2189 from Listeria innocua==		==Crystal structure of a hydrolase encoded by lin2189 from Listeria innocua==
-	<StructureSection load='5x5m' size='340' side='right' caption='[[5x5m]], [[Resolution\|resolution]] 1.21Å' scene=''>	+	<StructureSection load='5x5m' size='340' side='right'caption='[[5x5m]], [[Resolution\|resolution]] 1.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x5m]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5M OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X5M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x5m]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5M OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5X5M FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7YU:(+)-Yatakemycin'>7YU</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7YU:(+)-Yatakemycin'>7YU</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x5r\|5x5r]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x5r\|5x5r]]</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=5x5m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5m OCA], [http://pdbe.org/5x5m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5m RCSB], [http://www.ebi.ac.uk/pdbsum/5x5m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5m 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=5x5m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5m OCA], [http://pdbe.org/5x5m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5m RCSB], [http://www.ebi.ac.uk/pdbsum/5x5m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5m ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Zhang, J]]		[[Category: Zhang, J]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Hydrolase-antibiotic complex]]		[[Category: Hydrolase-antibiotic complex]]

OCA at 07:19, 6 December 2017

OCA — Wed, 06 Dec 2017 07:19:06 GMT

←Older revision		Revision as of 07:19, 6 December 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5x5m is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of a hydrolase encoded by lin2189 from Listeria innocua==
		+	<StructureSection load='5x5m' size='340' side='right' caption='[[5x5m]], [[Resolution\|resolution]] 1.21Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5x5m]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X5M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X5M FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7YU:(+)-Yatakemycin'>7YU</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x5r\|5x5r]]</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=5x5m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x5m OCA], [http://pdbe.org/5x5m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x5m RCSB], [http://www.ebi.ac.uk/pdbsum/5x5m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x5m ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	GyrI-like proteins are widely distributed in prokaryotes and eukaryotes, and recognized as small-molecule binding proteins. Here, we identify a subfamily of these proteins as cyclopropanoid cyclopropyl hydrolases (CCHs) that can catalyze the hydrolysis of the potent DNA-alkylating agents yatakemycin (YTM) and CC-1065. Co-crystallography and molecular dynamics simulation analyses reveal that these CCHs share a conserved aromatic cage for the hydrolytic activity. Subsequent cytotoxic assays confirm that CCHs are able to protect cells against YTM. Therefore, our findings suggest that the evolutionarily conserved GyrI-like proteins confer cellular protection against diverse xenobiotics via not only binding, but also catalysis.

-	~~Authors:~~ Zhang, J.	+	GyrI-like proteins catalyze cyclopropanoid hydrolysis to confer cellular protection.,Yuan H, Zhang J, Cai Y, Wu S, Yang K, Chan HCS, Huang W, Jin WB, Li Y, Yin Y, Igarashi Y, Yuan S, Zhou J, Tang GL Nat Commun. 2017 Nov 14;8(1):1485. doi: 10.1038/s41467-017-01508-1. PMID:29133784<ref>PMID:29133784</ref>

-	~~Description: Crystal structure of~~ a ~~hydrolase encoded by lin2189 from Listeria innocua~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5x5m" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Zhang, J]]		[[Category: Zhang, J]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase-antibiotic complex]]

OCA: Protected "5x5m" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 15:47:00 GMT

Protected "5x5m" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:47, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5x5m is ON HOLD until Paper Publication Authors: Zhang, J. Description: Crystal structure of a hydrolase encoded by lin2189 from Listeria innocua [...

OCA — Thu, 09 Mar 2017 15:46:59 GMT

New page: '''Unreleased structure''' The entry 5x5m is ON HOLD until Paper Publication Authors: Zhang, J. Description: Crystal structure of a hydrolase encoded by lin2189 from Listeria innocua [...

New page

'''Unreleased structure'''

The entry 5x5m is ON HOLD until Paper Publication

Authors: Zhang, J.

Description: Crystal structure of a hydrolase encoded by lin2189 from Listeria innocua
[[Category: Unreleased Structures]]
[[Category: Zhang, J]]