4xup - Revision history

OCA at 10:51, 10 January 2024

OCA — Wed, 10 Jan 2024 10:51:04 GMT

←Older revision		Revision as of 10:51, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xup]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenibacillus_barcinonensis Paenibacillus barcinonensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XUP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XUP FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xup]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenibacillus_barcinonensis Paenibacillus barcinonensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XUP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XUP 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=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]] 2.43Å</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=GOL:GLYCEROL'>GOL</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=4xup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xup OCA], [https://pdbe.org/4xup PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xup RCSB], [https://www.ebi.ac.uk/pdbsum/4xup PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xup 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=4xup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xup OCA], [https://pdbe.org/4xup PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xup RCSB], [https://www.ebi.ac.uk/pdbsum/4xup PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xup ProSAT]</span></td></tr>
	</table>		</table>

OCA at 17:53, 26 April 2023

OCA — Wed, 26 Apr 2023 17:53:22 GMT

←Older revision		Revision as of 17:53, 26 April 2023
Line 1:		Line 1:

	==Structure of the N-terminal CBM22-1-CBM22-2 tandem domain from Paenibacillus barcinonensis Xyn10C==		==Structure of the N-terminal CBM22-1-CBM22-2 tandem domain from Paenibacillus barcinonensis Xyn10C==
-	<StructureSection load='4xup' size='340' side='right' caption='[[4xup]], [[Resolution\|resolution]] 2.43Å' scene=''>	+	<StructureSection load='4xup' size='340' side='right'caption='[[4xup]], [[Resolution\|resolution]] 2.43Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xup]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacillus_sp._bp-23 Bacillus sp. bp-23~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XUP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XUP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xup]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenibacillus_barcinonensis Paenibacillus barcinonensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XUP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XUP 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=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=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">xynC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=198119 Bacillus sp. BP-23])</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=4xup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xup OCA], [https://pdbe.org/4xup PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xup RCSB], [https://www.ebi.ac.uk/pdbsum/4xup PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xup ProSAT]</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=4xup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xup OCA], [~~http~~://pdbe.org/4xup PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xup RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xup PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xup ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/XYNC_PAEBA XYNC_PAEBA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus sp. bp-23~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Endo-1,4-beta-xylanase~~]]	+	[[Category: Paenibacillus barcinonensis]]
-	[[Category: Sainz-Polo~~, M A~~]]	+	[[Category: Sainz-Polo MA]]
-	[[Category: Sanz-Aparicio, J]]	+	[[Category: Sanz-Aparicio J]]
-	~~[[Category: 4-beta-xylanase]]~~	+
-	~~[[Category: Binding site]]~~	+
-	~~[[Category: Carbohydrate]]~~	+
-	~~[[Category: Endo-1]]~~	+
-	~~[[Category: Enzyme stability]]~~	+
-	~~[[Category: Substrate specificity]]~~	+
-	~~[[Category: Sugar binding protein]]~~	+
-	~~[[Category: Thermophilic enzyme]]~~	+
-	~~[[Category: Thermostabilizing domain]]~~	+
-	~~[[Category: Xylan-binding domain~~]]	+

OCA at 06:14, 18 April 2018

OCA — Wed, 18 Apr 2018 06:14:19 GMT

←Older revision		Revision as of 06:14, 18 April 2018
Line 3:		Line 3:
	<StructureSection load='4xup' size='340' side='right' caption='[[4xup]], [[Resolution\|resolution]] 2.43Å' scene=''>		<StructureSection load='4xup' size='340' side='right' caption='[[4xup]], [[Resolution\|resolution]] 2.43Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xup]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XUP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XUP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xup]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp._bp-23 Bacillus sp. bp-23]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XUP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XUP 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=GOL:GLYCEROL'>GOL</scene></td></tr>		</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=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">xynC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=198119 Bacillus sp. BP-23])</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=4xup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xup OCA], [http://pdbe.org/4xup PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xup RCSB], [http://www.ebi.ac.uk/pdbsum/4xup PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xup 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=4xup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xup OCA], [http://pdbe.org/4xup PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xup RCSB], [http://www.ebi.ac.uk/pdbsum/4xup PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xup ProSAT]</span></td></tr>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus sp. bp-23]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Sainz-Polo, M A]]		[[Category: Sainz-Polo, M A]]

OCA at 14:19, 27 April 2017

OCA — Thu, 27 Apr 2017 14:19:37 GMT

←Older revision		Revision as of 14:19, 27 April 2017
Line 1:		Line 1:
		+
	==Structure of the N-terminal CBM22-1-CBM22-2 tandem domain from Paenibacillus barcinonensis Xyn10C==		==Structure of the N-terminal CBM22-1-CBM22-2 tandem domain from Paenibacillus barcinonensis Xyn10C==
	<StructureSection load='4xup' size='340' side='right' caption='[[4xup]], [[Resolution\|resolution]] 2.43Å' scene=''>		<StructureSection load='4xup' size='340' side='right' caption='[[4xup]], [[Resolution\|resolution]] 2.43Å' scene=''>
Line 5:		Line 6:
	</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=GOL:GLYCEROL'>GOL</scene></td></tr>		</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=GOL:GLYCEROL'>GOL</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=4xup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xup OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xup RCSB], [http://www.ebi.ac.uk/pdbsum/4xup 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=4xup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xup OCA], [http://pdbe.org/4xup PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xup RCSB], [http://www.ebi.ac.uk/pdbsum/4xup PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xup ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4xup" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:36, 3 June 2015

OCA — Wed, 03 Jun 2015 12:36:44 GMT

←Older revision		Revision as of 12:36, 3 June 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure of the N-terminal CBM22-1-CBM22-2 tandem domain from Paenibacillus barcinonensis Xyn10C==
		+	<StructureSection load='4xup' size='340' side='right' caption='[[4xup]], [[Resolution\|resolution]] 2.43Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xup]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XUP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XUP 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=GOL:GLYCEROL'>GOL</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='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=4xup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xup OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xup RCSB], [http://www.ebi.ac.uk/pdbsum/4xup PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Elucidating the molecular mechanisms regulating multimodularity is a challenging task. Paenibacillus barcinonensis Xyn10C is a 120 kD modular enzyme that presents the CBM22/GH10/CBM9 architecture found in a subset of large xylanases. We report here the three-dimensional structure of the Xyn10C N-terminal region, containing the xylan-binding CBM22-1-CBM22-2 tandem (Xyn10C-XBD), which represents the first solved crystal structure of two contiguous CBM22. Xyn10C-XBD is folded into two separate CBM22 modules linked by a flexible segment that endows the tandem with extraordinary plasticity. Each isolated domain have been expressed and crystallized and their binding abilities have been investigated. Both domains contain the RW/YYYE motif required for xylan binding. However, crystallographic analysis of CBM22-2 complexes shows Trp308 as an additional binding determinant. The long loop containing Trp308 creates a platform that possibly contributes to recognize precise decorations at subsite S2. CBM22-2 may thus define a subset of xylan-binding CBM22s directed to particular regions of the polysaccharide. Affinity electrophoresis reveals Xyn10C-XBD binds arabinoxylans more tightly, more apparent when CBM22-2 is tested against highly substituted xylan. The crystal structure of the catalytic domain, also reported, shows the capacity of the active site to accommodate xylan substitutions at almost all subsites. The structural differences found at both Xyn10C-XBD domains are consistent with the ITC experiments showing two sites with different affinities in the tandem. On the basis of the CBM22 distinct characteristics, a deliver strategy of Xyn10C mediated by Xyn10C-XBD is proposed.

-	~~The entry 4xup is ON HOLD until Paper Publication~~	+	Exploring multimodularity in plant cell wall deconstruction: structural and functional analysis of Xyn10C containing the CBM22-1-CBM22-2 tandem.,Sainz-Polo MA, Gonzalez B, Menendez M, Pastor FI, Sanz-Aparicio J J Biol Chem. 2015 May 22. pii: jbc.M115.659300. PMID:26001782<ref>PMID:26001782</ref>

-	~~Authors: Sainz-Polo~~, M.A.~~, Sanz-Aparicio, J~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Structure of the N-terminal CBM22~~-1-~~CBM22~~-~~2 tandem domain from Paenibacillus barcinonensis Xyn10C~~	+	== References ==
-	~~[[Category: Unreleased Structures~~]]	+	<references/>
-	[[Category: Sainz-Polo, M.A]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Endo-1,4-beta-xylanase]]
		+	[[Category: Sainz-Polo, M A]]
	[[Category: Sanz-Aparicio, J]]		[[Category: Sanz-Aparicio, J]]
		+	[[Category: 4-beta-xylanase]]
		+	[[Category: Binding site]]
		+	[[Category: Carbohydrate]]
		+	[[Category: Endo-1]]
		+	[[Category: Enzyme stability]]
		+	[[Category: Substrate specificity]]
		+	[[Category: Sugar binding protein]]
		+	[[Category: Thermophilic enzyme]]
		+	[[Category: Thermostabilizing domain]]
		+	[[Category: Xylan-binding domain]]

OCA at 12:24, 25 February 2015

OCA — Wed, 25 Feb 2015 12:24:37 GMT

←Older revision		Revision as of 12:24, 25 February 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xup is ON HOLD	+	The entry 4xup is ON HOLD until Paper Publication

	Authors: Sainz-Polo, M.A., Sanz-Aparicio, J.		Authors: Sainz-Polo, M.A., Sanz-Aparicio, J.

OCA: Protected "4xup" [edit=sysop:move=sysop]

OCA — Sat, 07 Feb 2015 14:50:49 GMT

Protected "4xup" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:50, 7 February 2015

OCA: New page: '''Unreleased structure''' The entry 4xup is ON HOLD Authors: Sainz-Polo, M.A., Sanz-Aparicio, J. Description: Structure of the N-terminal CBM22-1-CBM22-2 tandem domain from Paenibacil...

OCA — Sat, 07 Feb 2015 14:50:48 GMT

New page: '''Unreleased structure''' The entry 4xup is ON HOLD Authors: Sainz-Polo, M.A., Sanz-Aparicio, J. Description: Structure of the N-terminal CBM22-1-CBM22-2 tandem domain from Paenibacil...

New page

'''Unreleased structure'''

The entry 4xup is ON HOLD

Authors: Sainz-Polo, M.A., Sanz-Aparicio, J.

Description: Structure of the N-terminal CBM22-1-CBM22-2 tandem domain from Paenibacillus barcinonensis Xyn10C
[[Category: Unreleased Structures]]
[[Category: Sainz-Polo, M.A]]
[[Category: Sanz-Aparicio, J]]