1bfn - Revision history

OCA at 06:35, 7 February 2024

2024-02-07T06:35:58Z

←Older revision		Revision as of 06:35, 7 February 2024
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	<StructureSection load='1bfn' size='340' side='right'caption='[[1bfn]], [[Resolution\|resolution]] 2.07Å' scene=''>		<StructureSection load='1bfn' size='340' side='right'caption='[[1bfn]], [[Resolution\|resolution]] 2.07Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bfn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Glycine_hispida~~ Glycine ~~hispida~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BFN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BFN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bfn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BFN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BFN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GLC:ALPHA~~-~~D-GLUCOSE'>GLC</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]] 2.07Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https:~~/~~/en.wikipedia.org/wiki/Beta-amylase Beta-amylase]~~, ~~with EC number [https~~:~~//www.brenda~~-~~enzymes.info~~/~~php/result_flat.php4?ecno~~=~~3.2.1.2 3.2.1.2]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900012:beta-cyclodextrin'>PRD_900012</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1bfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bfn OCA], [https://pdbe.org/1bfn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bfn RCSB], [https://www.ebi.ac.uk/pdbsum/1bfn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bfn 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=1bfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bfn OCA], [https://pdbe.org/1bfn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bfn RCSB], [https://www.ebi.ac.uk/pdbsum/1bfn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bfn ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AMYB_SOYBN AMYB_SOYBN]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1bfn ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1bfn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	In order to study the interaction of soybean beta-amylase with substrate, we solved the crystal structure of beta-cyclodextrin-enzyme complex and compared it with that of alpha-cyclodextrin-enzyme complex. The enzyme was expressed in Escherichia coli at a high level as a soluble and catalytically active protein. The purified recombinant enzyme had properties nearly identical to those of native soybean beta-amylase and formed the same crystals as the native enzyme. The crystal structure of recombinant enzyme complexed with beta-cyclodextrin was refined at 2. 07-A resolution with a final crystallographic R value of 15.8% (Rfree = 21.1%). The root mean square deviation in the position of C-alpha atoms between this recombinant enzyme and the native enzyme was 0.22 A. These results indicate that the expression system established here is suitable for studying structure-function relationships of beta-amylase. The conformation of the bound beta-cyclodextrin takes an ellipsoid shape in contrast to the circular shape of the bound alpha-cyclodextrin. The cyclodextrins shared mainly two glucose binding sites, 3 and 4. The glucose residue 4 was slightly shifted from the maltose binding site. This suggests that the binding site of the cyclodextrins is important for its holding of a cleaved substrate, which enables the multiple attack mechanism of beta-amylase.
-
-	Crystal structure of recombinant soybean beta-amylase complexed with beta-cyclodextrin.,Adachi M, Mikami B, Katsube T, Utsumi S J Biol Chem. 1998 Jul 31;273(31):19859-65. PMID:9677422<ref>PMID:9677422</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1bfn" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Amylase 3D structures\|Amylase 3D structures]]		*[[Amylase 3D structures\|Amylase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	~~[[Category: Beta-amylase]]~~	+	[[Category: Glycine max]]
-	[[Category: Glycine ~~hispida~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Adachi, M]]	+	[[Category: Adachi M]]
-	[[Category: Katsube, T]]	+	[[Category: Katsube T]]
-	[[Category: Mikami, B]]	+	[[Category: Mikami B]]
-	[[Category: Utsumi, S]]	+	[[Category: Utsumi S]]
-	~~[[Category: Beta-cyclodextrin]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Recombinant~~]]	+

OCA at 15:07, 2 June 2021

2021-06-02T15:07:08Z

←Older revision		Revision as of 15:07, 2 June 2021
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	<StructureSection load='1bfn' size='340' side='right'caption='[[1bfn]], [[Resolution\|resolution]] 2.07Å' scene=''>		<StructureSection load='1bfn' size='340' side='right'caption='[[1bfn]], [[Resolution\|resolution]] 2.07Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bfn]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BFN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1BFN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bfn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BFN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BFN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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/Beta-amylase Beta-amylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.2 3.2.1.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-amylase Beta-amylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.2 3.2.1.2] </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=1bfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bfn OCA], [~~http~~://pdbe.org/1bfn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1bfn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1bfn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1bfn 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=1bfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bfn OCA], [https://pdbe.org/1bfn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bfn RCSB], [https://www.ebi.ac.uk/pdbsum/1bfn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bfn ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 16:15, 28 August 2019

2019-08-28T16:15:25Z

←Older revision		Revision as of 16:15, 28 August 2019
Line 1:		Line 1:

	==BETA-AMYLASE/BETA-CYCLODEXTRIN COMPLEX==		==BETA-AMYLASE/BETA-CYCLODEXTRIN COMPLEX==
-	<StructureSection load='1bfn' size='340' side='right' caption='[[1bfn]], [[Resolution\|resolution]] 2.07Å' scene=''>	+	<StructureSection load='1bfn' size='340' side='right'caption='[[1bfn]], [[Resolution\|resolution]] 2.07Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1bfn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BFN FirstGlance]. <br>		<table><tr><td colspan='2'>[[1bfn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BFN FirstGlance]. <br>
Line 12:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bf/1bfn_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bf/1bfn_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 27:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1bfn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1bfn" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Amylase 3D structures\|Amylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 36:
	[[Category: Beta-amylase]]		[[Category: Beta-amylase]]
	[[Category: Glycine hispida]]		[[Category: Glycine hispida]]
		+	[[Category: Large Structures]]
	[[Category: Adachi, M]]		[[Category: Adachi, M]]
	[[Category: Katsube, T]]		[[Category: Katsube, T]]

OCA at 11:03, 22 November 2017

2017-11-22T11:03:38Z

←Older revision		Revision as of 11:03, 22 November 2017
Line 1:		Line 1:
		+
	==BETA-AMYLASE/BETA-CYCLODEXTRIN COMPLEX==		==BETA-AMYLASE/BETA-CYCLODEXTRIN COMPLEX==
	<StructureSection load='1bfn' size='340' side='right' caption='[[1bfn]], [[Resolution\|resolution]] 2.07Å' scene=''>		<StructureSection load='1bfn' size='340' side='right' caption='[[1bfn]], [[Resolution\|resolution]] 2.07Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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=GLC:ALPHA-D-GLUCOSE'>GLC</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/Beta-amylase Beta-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.2 3.2.1.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-amylase Beta-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.2 3.2.1.2] </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=1bfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bfn OCA], [http://pdbe.org/1bfn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bfn RCSB], [http://www.ebi.ac.uk/pdbsum/1bfn PDBsum]</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=1bfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bfn OCA], [http://pdbe.org/1bfn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bfn RCSB], [http://www.ebi.ac.uk/pdbsum/1bfn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1bfn ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1bfn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1bfn" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Amylase\|Amylase]]
-	*[[User:Gabriel Pons/Sandbox 2\|User:Gabriel Pons/Sandbox 2]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:17, 10 February 2016

2016-02-10T07:17:46Z

←Older revision		Revision as of 07:17, 10 February 2016
Line 15:		Line 15:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1bfn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:37, 11 September 2015

2015-09-11T06:37:17Z

←Older revision		Revision as of 06:37, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1bfn' size='340' side='right' caption='[[1bfn]], [[Resolution\|resolution]] 2.07Å' scene=''>		<StructureSection load='1bfn' size='340' side='right' caption='[[1bfn]], [[Resolution\|resolution]] 2.07Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bfn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Glycine_max~~ Glycine ~~max~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BFN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bfn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BFN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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=GLC:ALPHA-D-GLUCOSE'>GLC</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/Beta-amylase Beta-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.2 3.2.1.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-amylase Beta-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.2 3.2.1.2] </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=1bfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bfn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bfn RCSB], [http://www.ebi.ac.uk/pdbsum/1bfn PDBsum]</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=1bfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bfn OCA], [http://pdbe.org/1bfn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bfn RCSB], [http://www.ebi.ac.uk/pdbsum/1bfn PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1bfn" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Beta-amylase]]		[[Category: Beta-amylase]]
-	[[Category: Glycine ~~max~~]]	+	[[Category: Glycine hispida]]
	[[Category: Adachi, M]]		[[Category: Adachi, M]]
	[[Category: Katsube, T]]		[[Category: Katsube, T]]

OCA at 11:23, 22 December 2014

2014-12-22T11:23:09Z

←Older revision		Revision as of 11:23, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1bfn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BFN FirstGlance]. <br>		<table><tr><td colspan='2'>[[1bfn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BFN FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-amylase Beta-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.2 3.2.1.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-amylase Beta-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.2 3.2.1.2] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1bfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bfn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bfn RCSB], [http://www.ebi.ac.uk/pdbsum/1bfn PDBsum]</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=1bfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bfn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bfn RCSB], [http://www.ebi.ac.uk/pdbsum/1bfn PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 28:
	==See Also==		==See Also==
	*[[Amylase\|Amylase]]		*[[Amylase\|Amylase]]
		+	*[[User:Gabriel Pons/Sandbox 2\|User:Gabriel Pons/Sandbox 2]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 35:
	[[Category: Beta-amylase]]		[[Category: Beta-amylase]]
	[[Category: Glycine max]]		[[Category: Glycine max]]
-	[[Category: Adachi, M.]]	+	[[Category: Adachi, M]]
-	[[Category: Katsube, T.]]	+	[[Category: Katsube, T]]
-	[[Category: Mikami, B.]]	+	[[Category: Mikami, B]]
-	[[Category: Utsumi, S~~.]]~~	+	[[Category: Utsumi, S]]
-	~~[[Category: Beta-amylase~~]]	+
	[[Category: Beta-cyclodextrin]]		[[Category: Beta-cyclodextrin]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Recombinant]]		[[Category: Recombinant]]

OCA at 03:06, 7 August 2014

2014-08-07T03:06:40Z

←Older revision		Revision as of 03:06, 7 August 2014
Line 1:		Line 1:
-	[[~~Image~~:1bfn.~~png\|left~~\|200px]]	+	==BETA-AMYLASE/BETA-CYCLODEXTRIN COMPLEX==
		+	<StructureSection load='1bfn' size='340' side='right' caption='[[1bfn]], [[Resolution\|resolution]] 2.07Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1bfn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BFN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BFN FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-amylase Beta-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.2 3.2.1.2] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1bfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bfn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bfn RCSB], [http://www.ebi.ac.uk/pdbsum/1bfn PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bf/1bfn_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In order to study the interaction of soybean beta-amylase with substrate, we solved the crystal structure of beta-cyclodextrin-enzyme complex and compared it with that of alpha-cyclodextrin-enzyme complex. The enzyme was expressed in Escherichia coli at a high level as a soluble and catalytically active protein. The purified recombinant enzyme had properties nearly identical to those of native soybean beta-amylase and formed the same crystals as the native enzyme. The crystal structure of recombinant enzyme complexed with beta-cyclodextrin was refined at 2. 07-A resolution with a final crystallographic R value of 15.8% (Rfree = 21.1%). The root mean square deviation in the position of C-alpha atoms between this recombinant enzyme and the native enzyme was 0.22 A. These results indicate that the expression system established here is suitable for studying structure-function relationships of beta-amylase. The conformation of the bound beta-cyclodextrin takes an ellipsoid shape in contrast to the circular shape of the bound alpha-cyclodextrin. The cyclodextrins shared mainly two glucose binding sites, 3 and 4. The glucose residue 4 was slightly shifted from the maltose binding site. This suggests that the binding site of the cyclodextrins is important for its holding of a cleaved substrate, which enables the multiple attack mechanism of beta-amylase.

-	~~{{STRUCTURE_1bfn\| PDB=1bfn \| SCENE= }}~~	+	Crystal structure of recombinant soybean beta-amylase complexed with beta-cyclodextrin.,Adachi M, Mikami B, Katsube T, Utsumi S J Biol Chem. 1998 Jul 31;273(31):19859-65. PMID:9677422<ref>PMID:9677422</ref>

-	~~===BETA-AMYLASE~~/~~BETA-CYCLODEXTRIN COMPLEX===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9677422}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1bfn]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Glycine_max Glycine max]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1BFN OCA].~~	+

	==See Also==		==See Also==
-	*[[~~Alpha-~~Amylase\|~~Alpha-~~Amylase]]	+	*[[Amylase\|Amylase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:009677422<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Beta-amylase]]		[[Category: Beta-amylase]]
	[[Category: Glycine max]]		[[Category: Glycine max]]

OCA at 16:47, 20 October 2012

2012-10-20T16:47:08Z

←Older revision		Revision as of 16:47, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1bfn]] is a 1 chain structure ~~of [[Alpha-Amylase]]~~ with sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BFN OCA].	+	[[1bfn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BFN OCA].

	==See Also==		==See Also==

OCA: Protected "1bfn" [edit=sysop:move=sysop]

2012-07-26T22:50:00Z

Protected "1bfn" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:50, 26 July 2012