1b3x - Revision history

OCA at 05:35, 9 August 2023

2023-08-09T05:35:55Z

←Older revision		Revision as of 05:35, 9 August 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1b3x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium simplicissimum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B3X FirstGlance]. <br>		<table><tr><td colspan='2'>[[1b3x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium simplicissimum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B3X FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=XYP:BETA~~-~~D-XYLOPYRANOSE'>XYP</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]] 2.2Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=PRD_900117:4beta-beta-xylotriose'>PRD_900117</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Endo~~-~~1,4~~-~~beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8]~~ </~~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=1b3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b3x OCA], [https://pdbe.org/1b3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b3x RCSB], [https://www.ebi.ac.uk/pdbsum/1b3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b3x 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=1b3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b3x OCA], [https://pdbe.org/1b3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b3x RCSB], [https://www.ebi.ac.uk/pdbsum/1b3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b3x ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/XYNA_PENSI XYNA_PENSI]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Penicillium simplicissimum]]		[[Category: Penicillium simplicissimum]]
-	[[Category: Kratky, C]]	+	[[Category: Kratky C]]
-	[[Category: Schmidt, A]]	+	[[Category: Schmidt A]]
-	~~[[Category: Family 10 xylanase]]~~	+
-	~~[[Category: Glycosyl hydrolase]]~~	+
-	~~[[Category: Substrate binding~~]]	+

OCA at 09:16, 29 September 2021

2021-09-29T09:16:45Z

←Older revision		Revision as of 09:16, 29 September 2021
Line 3:		Line 3:
	<StructureSection load='1b3x' size='340' side='right'caption='[[1b3x]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1b3x' size='340' side='right'caption='[[1b3x]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1b3x]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium simplicissimum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B3X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1B3X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1b3x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium simplicissimum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B3X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=1b3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b3x OCA], [~~http~~://pdbe.org/1b3x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1b3x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1b3x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1b3x 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=1b3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b3x OCA], [https://pdbe.org/1b3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b3x RCSB], [https://www.ebi.ac.uk/pdbsum/1b3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b3x ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 08:48, 21 May 2019

2019-05-21T08:48:54Z

←Older revision		Revision as of 08:48, 21 May 2019
Line 1:		Line 1:

	==XYLANASE FROM PENICILLIUM SIMPLICISSIMUM, COMPLEX WITH XYLOTRIOSE==		==XYLANASE FROM PENICILLIUM SIMPLICISSIMUM, COMPLEX WITH XYLOTRIOSE==
-	<StructureSection load='1b3x' size='340' side='right' caption='[[1b3x]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='1b3x' size='340' side='right'caption='[[1b3x]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1b3x]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium simplicissimum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B3X FirstGlance]. <br>		<table><tr><td colspan='2'>[[1b3x]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium simplicissimum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B3X FirstGlance]. <br>
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b3/1b3x_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b3/1b3x_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 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
		+	[[Category: Large Structures]]
	[[Category: Penicillium simplicissimum]]		[[Category: Penicillium simplicissimum]]
	[[Category: Kratky, C]]		[[Category: Kratky, C]]

OCA at 06:11, 17 August 2017

2017-08-17T06:11:23Z

←Older revision		Revision as of 06:11, 17 August 2017
Line 1:		Line 1:
		+
	==XYLANASE FROM PENICILLIUM SIMPLICISSIMUM, COMPLEX WITH XYLOTRIOSE==		==XYLANASE FROM PENICILLIUM SIMPLICISSIMUM, COMPLEX WITH XYLOTRIOSE==
	<StructureSection load='1b3x' size='340' side='right' caption='[[1b3x]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1b3x' size='340' side='right' caption='[[1b3x]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=1b3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b3x OCA], [http://pdbe.org/1b3x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1b3x RCSB], [http://www.ebi.ac.uk/pdbsum/1b3x 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=1b3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b3x OCA], [http://pdbe.org/1b3x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1b3x RCSB], [http://www.ebi.ac.uk/pdbsum/1b3x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1b3x ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 17:
	<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=1b3x ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:23, 11 September 2015

2015-09-11T08:23:46Z

←Older revision		Revision as of 08:23, 11 September 2015
Line 6:		Line 6:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=1b3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b3x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b3x RCSB], [http://www.ebi.ac.uk/pdbsum/1b3x 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=1b3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b3x OCA], [http://pdbe.org/1b3x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1b3x RCSB], [http://www.ebi.ac.uk/pdbsum/1b3x PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 1b3x" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:46, 22 December 2014

2014-12-22T09:46:26Z

OCA at 03:18, 7 August 2014

2014-08-07T03:18:26Z

←Older revision		Revision as of 03:18, 7 August 2014
Line 1:		Line 1:
-	[[~~Image:~~1b3x.~~png~~\|~~left~~\|200px]]	+	==XYLANASE FROM PENICILLIUM SIMPLICISSIMUM, COMPLEX WITH XYLOTRIOSE==
		+	<StructureSection load='1b3x' size='340' side='right' caption='[[1b3x]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1b3x]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium simplicissimum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B3X FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=1b3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b3x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b3x RCSB], [http://www.ebi.ac.uk/pdbsum/1b3x 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/b3/1b3x_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 ==
		+	Following a recent low-temperature crystal structure analysis of the native xylanase from Penicillium simplicissimum [Schmidt et al. (1998) Protein Sci. 7, 2081-2088], where an array of glycerol molecules, diffused into the crystal during soaking in a cryoprotectant, was observed within the active-site cleft, we utilized monomeric xylose as well as a variety of linear (Xn, n = 2 to 5) and branched xylooligomers at high concentrations (typically 20% w/v) as cryoprotectant for low-temperature crystallographic experiments. Binding of the glycosidic moiety (or its hydrolysis products) to the enzyme's active-site cleft was observed after as little as 30 s soaking of a native enzyme crystal. The use of a substrate or substrate analogue as cryoprotectant therefore suggests itself as a simple and widely applicable alternative to the use of crystallographic flow-cells for substrate-saturation experiments. Short-chain xylooligomers, i.e., xylobiose (X2) and xylotriose (X3), were found to bind to the active-site cleft with its reducing end hydrogen-bonded to the catalytic acid-base catalyst Glu132. Xylotetraose (X4) and -pentaose (X5) had apparently been cleaved during the soaking time into a xylotriose plus a monomeric (X4) or dimeric (X5) sugar. While the trimeric hydrolysis product was always found to bind in the same way as xylotriose, the monomer or dimer yielded only weak and diffuse electron density within the xylan-binding cleft, at the opposite side of the active center. This suggests that the two catalytic residues divide the binding cleft into a "substrate recognition area" (from the active site toward the nonreducing end of a bound xylan chain), with strong and specific xylan binding and a "product release area" with considerably weaker and less specific binding. The size of the substrate recognition area (3-4 subsites for sugar rings) explains enzyme kinetic data, according to which short oligomers (X2 and X3) bind to the enzyme without being hydrolyzed.

-	~~{{STRUCTURE_1b3x\| PDB=1b3x \| SCENE= }}~~	+	Xylan binding subsite mapping in the xylanase from Penicillium simplicissimum using xylooligosaccharides as cryo-protectant.,Schmidt A, Gubitz GM, Kratky C Biochemistry. 1999 Feb 23;38(8):2403-12. PMID:10029534<ref>PMID:10029534</ref>

-	~~===XYLANASE FROM PENICILLIUM SIMPLICISSIMUM~~, ~~COMPLEX WITH XYLOTRIOSE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10029534}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1b3x]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Penicillium_simplicissimum Penicillium simplicissimum]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1B3X OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:010029534<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Penicillium simplicissimum]]		[[Category: Penicillium simplicissimum]]

OCA: Protected "1b3x" [edit=sysop:move=sysop]

2012-10-21T11:56:50Z

Protected "1b3x" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:56, 21 October 2012

OCA at 11:56, 21 October 2012

2012-10-21T11:56:47Z

←Older revision		Revision as of 11:56, 21 October 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1b3x.png\|left\|200px]]		[[Image:1b3x.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1b3x", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1b3x\| PDB=1b3x \| SCENE= }}		{{STRUCTURE_1b3x\| PDB=1b3x \| SCENE= }}

	===XYLANASE FROM PENICILLIUM SIMPLICISSIMUM, COMPLEX WITH XYLOTRIOSE===		===XYLANASE FROM PENICILLIUM SIMPLICISSIMUM, COMPLEX WITH XYLOTRIOSE===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_10029534}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 10029534 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_10029534}}		{{ABSTRACT_PUBMED_10029534}}

	==About this Structure==		==About this Structure==
-	~~1B3X~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium simplicissimum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B3X OCA].	+	[[1b3x]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium simplicissimum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B3X OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~10029534~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:010029534</ref><references group="xtra"/>
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Penicillium simplicissimum]]		[[Category: Penicillium simplicissimum]]
Line 32:		Line 20:
	[[Category: Penicillium simplicissimum]]		[[Category: Penicillium simplicissimum]]
	[[Category: Substrate binding]]		[[Category: Substrate binding]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:52:11 2009''

OCA at 15:52, 17 February 2009

2009-02-17T15:52:12Z

←Older revision		Revision as of 15:52, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1B3X is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium simplicissimum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B3X OCA].	+	1B3X is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium simplicissimum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B3X OCA].

	==Reference==		==Reference==
-	~~Xylan binding subsite mapping in the xylanase from Penicillium simplicissimum using xylooligosaccharides as cryo-protectant., Schmidt A, Gubitz GM, Kratky C, Biochemistry. 1999 Feb 23;38(8):2403-12.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/10029534 10029534]~~	+	<ref group="xtra">PMID:10029534</ref><references group="xtra"/>
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Penicillium simplicissimum]]		[[Category: Penicillium simplicissimum]]
-	[[Category: Single protein]]
	[[Category: Kratky, C.]]		[[Category: Kratky, C.]]
	[[Category: Schmidt, A.]]		[[Category: Schmidt, A.]]
Line 34:		Line 33:
	[[Category: Substrate binding]]		[[Category: Substrate binding]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jun 30 18~~:11:~~42 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:52:11 2009''

←Older revision		Revision as of 09:46, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1b3x]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium simplicissimum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B3X FirstGlance]. <br>		<table><tr><td colspan='2'>[[1b3x]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium simplicissimum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B3X FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=1b3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b3x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b3x RCSB], [http://www.ebi.ac.uk/pdbsum/1b3x 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=1b3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b3x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b3x RCSB], [http://www.ebi.ac.uk/pdbsum/1b3x 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 32:		Line 32:
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Penicillium simplicissimum]]		[[Category: Penicillium simplicissimum]]
-	[[Category: Kratky, C.]]	+	[[Category: Kratky, C]]
-	[[Category: Schmidt, A.]]	+	[[Category: Schmidt, A]]
	[[Category: Family 10 xylanase]]		[[Category: Family 10 xylanase]]
	[[Category: Glycosyl hydrolase]]		[[Category: Glycosyl hydrolase]]
-	[[Category: Penicillium simplicissimum]]
	[[Category: Substrate binding]]		[[Category: Substrate binding]]