5ghl - Revision history

OCA at 11:31, 2 August 2023

OCA — Wed, 02 Aug 2023 11:31:37 GMT

←Older revision		Revision as of 11:31, 2 August 2023
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	<StructureSection load='5ghl' size='340' side='right'caption='[[5ghl]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5ghl' size='340' side='right'caption='[[5ghl]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ghl]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~A._niger A.~~ niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GHL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GHL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ghl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GHL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GHL FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'>GOL</scene~~>, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>GLAA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~5061 A. niger])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Glucan_1,4-alpha-glucosidase Glucan 1,4-alpha-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.3 3.2.1.3]~~ </~~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=5ghl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ghl OCA], [https://pdbe.org/5ghl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ghl RCSB], [https://www.ebi.ac.uk/pdbsum/5ghl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ghl 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=5ghl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ghl OCA], [~~http~~://pdbe.org/5ghl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ghl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ghl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ghl ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AMYG_ASPNG AMYG_ASPNG]
	<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: A. niger]]	+	[[Category: Aspergillus niger]]
-	~~[[Category: Glucan 1,4-alpha-glucosidase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kusunoki, M]]	+	[[Category: Kusunoki M]]
-	[[Category: Miyake, H]]	+	[[Category: Miyake H]]
-	[[Category: Muraki, N]]	+	[[Category: Muraki N]]
-	[[Category: Suyama, Y]]	+	[[Category: Suyama Y]]
-	[[Category: Tanaka, A]]	+	[[Category: Tanaka A]]
-	~~[[Category: Beta-sheet structure]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 11:38, 25 December 2019

OCA — Wed, 25 Dec 2019 11:38:57 GMT

←Older revision		Revision as of 11:38, 25 December 2019
Line 1:		Line 1:

	==Crystal structure Analysis of the starch-binding domain of glucoamylase from Aspergillus niger==		==Crystal structure Analysis of the starch-binding domain of glucoamylase from Aspergillus niger==
-	<StructureSection load='5ghl' size='340' side='right' caption='[[5ghl]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5ghl' size='340' side='right'caption='[[5ghl]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ghl]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GHL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GHL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ghl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/A._niger A. niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GHL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GHL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLAA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5061 A. niger])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucan_1,4-alpha-glucosidase Glucan 1,4-alpha-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.3 3.2.1.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucan_1,4-alpha-glucosidase Glucan 1,4-alpha-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.3 3.2.1.3] </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=5ghl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ghl OCA], [http://pdbe.org/5ghl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ghl RCSB], [http://www.ebi.ac.uk/pdbsum/5ghl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ghl 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=5ghl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ghl OCA], [http://pdbe.org/5ghl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ghl RCSB], [http://www.ebi.ac.uk/pdbsum/5ghl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ghl ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glucoamylases are widely used commercially to produce glucose syrup from starch. The starch-binding domain (SBD) of glucoamylase from Aspergillus niger is a small globular protein containing a disulfide bond. The structure of A. niger SBD has been determined by NMR, but the conformation surrounding the disulfide bond was unclear. Therefore, X-ray crystal structural analysis was used to attempt to clarify the conformation of this region. The SBD was purified from an Escherichia coli-based expression system and crystallized at 293 K. The initial phase was determined by the molecular-replacement method, and the asymmetric unit of the crystal contained four protomers, two of which were related by a noncrystallographic twofold axis. Finally, the structure was solved at 2.0 A resolution. The SBD consisted of seven beta-strands and eight loops, and the conformation surrounding the disulfide bond was determined from a clear electron-density map. Comparison of X-ray- and NMR-determined structures of the free SBD showed no significant difference in the conformation of each beta-strand, but the conformations of the loops containing the disulfide bond and the L5 loop were different. In particular, the difference in the position of the C(alpha) atom of Cys509 between the X-ray- and NMR-determined structures was 13.3 A. In addition, the B factors of the amino-acid residues surrounding the disulfide bond are higher than those of other residues. Therefore, the conformation surrounding the disulfide bond is suggested to be highly flexible.
		+
		+	Crystal structure of the starch-binding domain of glucoamylase from Aspergillus niger.,Suyama Y, Muraki N, Kusunoki M, Miyake H Acta Crystallogr F Struct Biol Commun. 2017 Oct 1;73(Pt 10):550-554. doi:, 10.1107/S2053230X17012894. Epub 2017 Sep 23. PMID:28994402<ref>PMID:28994402</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ghl" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Alpha-glucosidase 3D structures\|Alpha-glucosidase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: A. niger]]
	[[Category: Glucan 1,4-alpha-glucosidase]]		[[Category: Glucan 1,4-alpha-glucosidase]]
		+	[[Category: Large Structures]]
	[[Category: Kusunoki, M]]		[[Category: Kusunoki, M]]
	[[Category: Miyake, H]]		[[Category: Miyake, H]]

OCA at 07:09, 18 October 2017

OCA — Wed, 18 Oct 2017 07:09:12 GMT

←Older revision		Revision as of 07:09, 18 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5ghl is ON HOLD until Paper Publication~~	+	==Crystal structure Analysis of the starch-binding domain of glucoamylase from Aspergillus niger==
-		+	<StructureSection load='5ghl' size='340' side='right' caption='[[5ghl]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors: Miyake, H., Suyama, Y., Muraki, N., Kusunoki, M., Tanaka, A.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ghl]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GHL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GHL FirstGlance]. <br>
-	~~Description:~~ Crystal structure Analysis of the starch-binding domain of glucoamylase from Aspergillus niger	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucan_1,4-alpha-glucosidase Glucan 1,4-alpha-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.3 3.2.1.3] </span></td></tr>
-	[[Category: ~~Tanaka~~, A]]	+	<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=5ghl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ghl OCA], [http://pdbe.org/5ghl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ghl RCSB], [http://www.ebi.ac.uk/pdbsum/5ghl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ghl ProSAT]</span></td></tr>
-	[[Category: ~~Suyama~~, Y]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Glucan 1,4-alpha-glucosidase]]
		+	[[Category: Kusunoki, M]]
	[[Category: Miyake, H]]		[[Category: Miyake, H]]
	[[Category: Muraki, N]]		[[Category: Muraki, N]]
-	[[Category: ~~Kusunoki~~, M]]	+	[[Category: Suyama, Y]]
		+	[[Category: Tanaka, A]]
		+	[[Category: Beta-sheet structure]]
		+	[[Category: Hydrolase]]

OCA at 06:35, 10 May 2017

OCA — Wed, 10 May 2017 06:35:32 GMT

←Older revision		Revision as of 06:35, 10 May 2017
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	Description: Crystal structure Analysis of the starch-binding domain of glucoamylase from Aspergillus niger		Description: Crystal structure Analysis of the starch-binding domain of glucoamylase from Aspergillus niger
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Tanaka, A]]
	[[Category: Suyama, Y]]		[[Category: Suyama, Y]]
	[[Category: Miyake, H]]		[[Category: Miyake, H]]
	[[Category: Muraki, N]]		[[Category: Muraki, N]]
	[[Category: Kusunoki, M]]		[[Category: Kusunoki, M]]
-	[[Category: Tanaka, A]]

OCA at 08:54, 9 March 2017

OCA — Thu, 09 Mar 2017 08:54:41 GMT

←Older revision		Revision as of 08:54, 9 March 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Miyake, H., Suyama, Y., Muraki, N., Kusunoki, M., Tanaka, A.		Authors: Miyake, H., Suyama, Y., Muraki, N., Kusunoki, M., Tanaka, A.

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

OCA — Tue, 12 Jul 2016 21:33:59 GMT

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

←Older revision

Revision as of 21:33, 12 July 2016

OCA: New page: '''Unreleased structure''' The entry 5ghl is ON HOLD Authors: Miyake, H., Suyama, Y., Muraki, N., Kusunoki, M., Tanaka, A. Description: Crystal structure Analysis of the starch-binding...

OCA — Tue, 12 Jul 2016 21:33:57 GMT

New page: '''Unreleased structure''' The entry 5ghl is ON HOLD Authors: Miyake, H., Suyama, Y., Muraki, N., Kusunoki, M., Tanaka, A. Description: Crystal structure Analysis of the starch-binding...

New page

'''Unreleased structure'''

The entry 5ghl is ON HOLD

Authors: Miyake, H., Suyama, Y., Muraki, N., Kusunoki, M., Tanaka, A.

Description: Crystal structure Analysis of the starch-binding domain of glucoamylase from Aspergillus niger
[[Category: Unreleased Structures]]
[[Category: Suyama, Y]]
[[Category: Miyake, H]]
[[Category: Muraki, N]]
[[Category: Kusunoki, M]]
[[Category: Tanaka, A]]