5y6t - Revision history

OCA at 08:23, 22 November 2023

OCA — Wed, 22 Nov 2023 08:23:38 GMT

←Older revision		Revision as of 08:23, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5y6t' size='340' side='right'caption='[[5y6t]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5y6t' size='340' side='right'caption='[[5y6t]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y6t]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Eisfe Eisfe~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y6T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y6T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y6t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Eisenia_fetida Eisenia fetida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y6T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y6T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.7Å</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=5y6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y6t OCA], [~~http~~://pdbe.org/5y6t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y6t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y6t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y6t ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=5y6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y6t OCA], [https://pdbe.org/5y6t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y6t RCSB], [https://www.ebi.ac.uk/pdbsum/5y6t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y6t ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A3B6UEQ6_EISFE A0A3B6UEQ6_EISFE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Eisfe~~]]	+	[[Category: Eisenia fetida]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hirano, Y]]	+	[[Category: Hirano Y]]
-	[[Category: Tamada, T]]	+	[[Category: Tamada T]]
-	[[Category: Ueda, M]]	+	[[Category: Ueda M]]
-	~~[[Category: Carbohydrate]]~~	+
-	~~[[Category: Cold adaptation]]~~	+
-	~~[[Category: Gh5 family~~]]	+

OCA at 12:42, 25 December 2019

OCA — Wed, 25 Dec 2019 12:42:03 GMT

←Older revision		Revision as of 12:42, 25 December 2019
Line 1:		Line 1:

	==Crystal structure of endo-1,4-beta-mannanase from Eisenia fetida==		==Crystal structure of endo-1,4-beta-mannanase from Eisenia fetida==
-	<StructureSection load='5y6t' size='340' side='right' caption='[[5y6t]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5y6t' size='340' side='right'caption='[[5y6t]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y6t]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y6T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y6T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y6t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Eisfe Eisfe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y6T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y6T FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=5y6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y6t OCA], [http://pdbe.org/5y6t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y6t RCSB], [http://www.ebi.ac.uk/pdbsum/5y6t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y6t 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=5y6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y6t OCA], [http://pdbe.org/5y6t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y6t RCSB], [http://www.ebi.ac.uk/pdbsum/5y6t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y6t ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The endo-1,4-beta-mannanases (Ef-Man) gene from Eisenia fetida was determined to consist of 1131bp and encode a 377 amino acid protein. The amino acid sequence showed similarity with the endo-1,4-beta-mannanases of Daphnia pulex (62%), Cryptopygus antarcticus (64%), Crassostrea gigas (61%), Mytilus edulis (60%), and Aplysia kurodai (58%). The gene encoding mature Ef-Man was expressed in Pichia pastoris (GS115 strain). Based on SDS-PAGE analysis, the molecular mass of the purified recombinant Ef-Man (rEf-Man) was estimated to be 39kDa. All catalytically important residues of endo-1,4-beta-mannanases in the glycoside hydrolase (GH) family 5 were conserved in Ef-Man. The optimal temperature for rEf-Man was identified as 60 degrees C. HPLC and HPAEC analyses suggest that Ef-Man requires at least six subsites for efficient hydrolysis and is capable of performing transglycosylation reactions. The overall structure of rEf-Man is similar to those of GH5 family proteins, and tertiary structures around the active site are conserved among endo-1,4-beta-mannanase families. X-ray crystallographic analysis supports the hydrolysis and transglycosylation reaction mechanism determined by HPLC and HPAEC analyses.
		+
		+	Gene cloning, expression, and X-ray crystallographic analysis of a beta-mannanase from Eisenia fetida.,Ueda M, Hirano Y, Fukuhara H, Naka Y, Nakazawa M, Sakamoto T, Ogata Y, Tamada T Enzyme Microb Technol. 2018 Oct;117:15-22. doi: 10.1016/j.enzmictec.2018.05.014. , Epub 2018 May 25. PMID:30037547<ref>PMID:30037547</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5y6t" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Eisfe]]
		+	[[Category: Large Structures]]
	[[Category: Hirano, Y]]		[[Category: Hirano, Y]]
	[[Category: Tamada, T]]		[[Category: Tamada, T]]

OCA at 05:31, 27 June 2018

OCA — Wed, 27 Jun 2018 05:31:24 GMT

←Older revision		Revision as of 05:31, 27 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5y6t is ON HOLD until Paper Publication~~	+	==Crystal structure of endo-1,4-beta-mannanase from Eisenia fetida==
-		+	<StructureSection load='5y6t' size='340' side='right' caption='[[5y6t]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~Authors: Hirano, Y., Ueda, M., Tamada, T.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5y6t]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y6T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y6T FirstGlance]. <br>
-	~~Description:~~ Crystal structure of endo-1,4-beta-mannanase from Eisenia fetida	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=5y6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y6t OCA], [http://pdbe.org/5y6t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y6t RCSB], [http://www.ebi.ac.uk/pdbsum/5y6t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y6t ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hirano, Y]]
	[[Category: Tamada, T]]		[[Category: Tamada, T]]
	[[Category: Ueda, M]]		[[Category: Ueda, M]]
-	[[Category: ~~Hirano, Y~~]]	+	[[Category: Carbohydrate]]
		+	[[Category: Cold adaptation]]
		+	[[Category: Gh5 family]]

OCA at 05:21, 11 October 2017

OCA — Wed, 11 Oct 2017 05:21:10 GMT

←Older revision		Revision as of 05:21, 11 October 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5y6t is ON HOLD	+	The entry 5y6t is ON HOLD until Paper Publication

	Authors: Hirano, Y., Ueda, M., Tamada, T.		Authors: Hirano, Y., Ueda, M., Tamada, T.

OCA: Protected "5y6t" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:12:52 GMT

Protected "5y6t" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:12, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5y6t is ON HOLD Authors: Hirano, Y., Ueda, M., Tamada, T. Description: Crystal structure of endo-1,4-beta-mannanase from Eisenia fetida [[Category:...

OCA — Wed, 27 Sep 2017 16:12:51 GMT

New page: '''Unreleased structure''' The entry 5y6t is ON HOLD Authors: Hirano, Y., Ueda, M., Tamada, T. Description: Crystal structure of endo-1,4-beta-mannanase from Eisenia fetida [[Category:...

New page

'''Unreleased structure'''

The entry 5y6t is ON HOLD

Authors: Hirano, Y., Ueda, M., Tamada, T.

Description: Crystal structure of endo-1,4-beta-mannanase from Eisenia fetida
[[Category: Unreleased Structures]]
[[Category: Tamada, T]]
[[Category: Ueda, M]]
[[Category: Hirano, Y]]