5ynh - Revision history

OCA at 08:33, 22 November 2023

2023-11-22T08:33:33Z

←Older revision		Revision as of 08:33, 22 November 2023
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	<StructureSection load='5ynh' size='340' side='right'caption='[[5ynh]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='5ynh' size='340' side='right'caption='[[5ynh]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ynh]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YNH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YNH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ynh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YNH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YNH FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.05Å</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=5ynh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ynh OCA], [~~http~~://pdbe.org/5ynh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ynh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ynh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ynh ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PRD_900042:gamma-cyclodextrin'>PRD_900042</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=5ynh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ynh OCA], [https://pdbe.org/5ynh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ynh RCSB], [https://www.ebi.ac.uk/pdbsum/5ynh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ynh ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/W9BQ28_KLEPN W9BQ28_KLEPN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	[[Category: Klebsiella pneumoniae]]		[[Category: Klebsiella pneumoniae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Iwamoto, H]]	+	[[Category: Iwamoto H]]
-	[[Category: Mikami, B]]	+	[[Category: Mikami B]]
-	[[Category: Mizutani, K]]	+	[[Category: Mizutani K]]
-	[[Category: Saka, N]]	+	[[Category: Saka N]]
-	[[Category: Takahashi, N]]	+	[[Category: Takahashi N]]
-	~~[[Category: Alpha-amylase]]~~	+
-	~~[[Category: Co-crystallization]]~~	+
-	~~[[Category: Crystal]]~~	+
-	~~[[Category: Gamma-cyclodextrin]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pullulanase~~]]	+

OCA at 09:23, 21 October 2020

2020-10-21T09:23:15Z

←Older revision		Revision as of 09:23, 21 October 2020
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	==Crystal structure of Pullulanase from Klebsiella pneumoniae complex at 10 mM gamma-cyclodextrin==		==Crystal structure of Pullulanase from Klebsiella pneumoniae complex at 10 mM gamma-cyclodextrin==
-	<StructureSection load='5ynh' size='340' side='right' caption='[[5ynh]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='5ynh' size='340' side='right'caption='[[5ynh]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ynh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YNH OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YNH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ynh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YNH OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YNH FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=5ynh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ynh OCA], [http://pdbe.org/5ynh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ynh RCSB], [http://www.ebi.ac.uk/pdbsum/5ynh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ynh 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=5ynh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ynh OCA], [http://pdbe.org/5ynh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ynh RCSB], [http://www.ebi.ac.uk/pdbsum/5ynh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ynh ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Klebsiella pneumoniae]]		[[Category: Klebsiella pneumoniae]]
		+	[[Category: Large Structures]]
	[[Category: Iwamoto, H]]		[[Category: Iwamoto, H]]
	[[Category: Mikami, B]]		[[Category: Mikami, B]]

OCA at 08:53, 14 November 2018

2018-11-14T08:53:27Z

←Older revision		Revision as of 08:53, 14 November 2018
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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=5ynh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ynh OCA], [http://pdbe.org/5ynh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ynh RCSB], [http://www.ebi.ac.uk/pdbsum/5ynh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ynh 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=5ynh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ynh OCA], [http://pdbe.org/5ynh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ynh RCSB], [http://www.ebi.ac.uk/pdbsum/5ynh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ynh ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Crystal structures of Klebsiella pneumoniae pullulanase (KPP) in complex with alpha-cyclodextrin (alpha-CD), beta-cyclodextrin (beta-CD) and gamma-cyclodextrin (gamma-CD) were refined at around 1.98-2.59 A resolution from data collected at SPring-8. In the structures of the complexes obtained with 1 mM alpha-CD or gamma-CD, one molecule of CD was found at carbohydrate-binding module 41 only (CBM41). In the structures of the complexes obtained with 1 mM beta-CD or with 10 mM alpha-CD or gamma-CD, two molecules of CD were found at CBM41 and in the active-site cleft, where the hydrophobic residue of Phe746 occupies the inside cavity of the CD rings. In contrast to alpha-CD and gamma-CD, one beta-CD molecule was found at the active site only in the presence of 0.1 mM beta-CD. These results were coincident with the solution experiments, which showed that beta-CD inhibits this enzyme more than a thousand times more potently than alpha-CD and gamma-CD. The strong inhibition of beta-CD is caused by the optimized interaction between beta-CD and the side chain of Phe746. The increased Ki values of the F746A mutant for beta-CD supported the importance of Phe746 in the strong interaction of pullulanase with beta-CD.
		+
		+	Elucidation of the mechanism of interaction between Klebsiella pneumoniae pullulanase and cyclodextrin.,Saka N, Iwamoto H, Malle D, Takahashi N, Mizutani K, Mikami B Acta Crystallogr D Struct Biol. 2018 Nov 1;74(Pt 11):1115-1123. doi:, 10.1107/S2059798318014523. Epub 2018 Oct 30. PMID:30387770<ref>PMID:30387770</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ynh" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:46, 24 October 2018

2018-10-24T05:46:19Z

←Older revision		Revision as of 05:46, 24 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ynh ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of Pullulanase from Klebsiella pneumoniae complex at 10 mM gamma-cyclodextrin==
-		+	<StructureSection load='5ynh' size='340' side='right' caption='[[5ynh]], [[Resolution\|resolution]] 2.05Å' scene=''>
-	~~Authors~~: ~~Saka, N~~., ~~Iwamoto~~, H., ~~Takahashi~~, N., ~~Mizutani~~, K., ~~Mikami, B~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ynh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YNH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YNH FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of Pullulanase from~~ Klebsiella pneumoniae ~~complex at 10 mM gamma-cyclodextrin~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=5ynh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ynh OCA], [http://pdbe.org/5ynh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ynh RCSB], [http://www.ebi.ac.uk/pdbsum/5ynh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ynh ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Klebsiella pneumoniae]]
		+	[[Category: Iwamoto, H]]
		+	[[Category: Mikami, B]]
	[[Category: Mizutani, K]]		[[Category: Mizutani, K]]
-	[[Category: Iwamoto, H]]
	[[Category: Saka, N]]		[[Category: Saka, N]]
-	[[Category: Mikami, B]]
	[[Category: Takahashi, N]]		[[Category: Takahashi, N]]
		+	[[Category: Alpha-amylase]]
		+	[[Category: Co-crystallization]]
		+	[[Category: Crystal]]
		+	[[Category: Gamma-cyclodextrin]]
		+	[[Category: Hydrolase]]
		+	[[Category: Pullulanase]]

OCA at 04:54, 29 November 2017

2017-11-29T04:54:52Z

←Older revision		Revision as of 04:54, 29 November 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Saka, N., Iwamoto, H., Takahashi, N., Mizutani, K., Mikami, B.		Authors: Saka, N., Iwamoto, H., Takahashi, N., Mizutani, K., Mikami, B.

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

2017-11-01T04:47:35Z

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

←Older revision

Revision as of 04:47, 1 November 2017

OCA: New page: '''Unreleased structure''' The entry 5ynh is ON HOLD Authors: Saka, N., Iwamoto, H., Takahashi, N., Mizutani, K., Mikami, B. Description: Crystal structure of Pullulanase from Klebsiel...

2017-11-01T04:47:33Z

New page: '''Unreleased structure''' The entry 5ynh is ON HOLD Authors: Saka, N., Iwamoto, H., Takahashi, N., Mizutani, K., Mikami, B. Description: Crystal structure of Pullulanase from Klebsiel...

New page

'''Unreleased structure'''

The entry 5ynh is ON HOLD

Authors: Saka, N., Iwamoto, H., Takahashi, N., Mizutani, K., Mikami, B.

Description: Crystal structure of Pullulanase from Klebsiella pneumoniae complex at 10 mM gamma-cyclodextrin
[[Category: Unreleased Structures]]
[[Category: Mizutani, K]]
[[Category: Iwamoto, H]]
[[Category: Saka, N]]
[[Category: Mikami, B]]
[[Category: Takahashi, N]]