7k4s - Revision history

OCA at 15:17, 18 October 2023

OCA — Wed, 18 Oct 2023 15:17:34 GMT

←Older revision		Revision as of 15:17, 18 October 2023
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	<StructureSection load='7k4s' size='340' side='right'caption='[[7k4s]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='7k4s' size='340' side='right'caption='[[7k4s]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7k4s]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Theau Theau~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7K4S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7K4S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7k4s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoascus_aurantiacus Thermoascus aurantiacus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7K4S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7K4S FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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"~~>XYNA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~5087 THEAU])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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/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'>[https://proteopedia.org/fgij/fg.htm?mol=7k4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k4s OCA], [https://pdbe.org/7k4s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k4s RCSB], [https://www.ebi.ac.uk/pdbsum/7k4s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k4s ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=7k4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k4s OCA], [~~http~~://pdbe.org/7k4s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7k4s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7k4s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7k4s ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/XYNA_THEAU XYNA_THEAU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 7k4s" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7k4s" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Kemp eliminase\|Kemp eliminase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Theau~~]]	+	[[Category: Thermoascus aurantiacus]]
-	[[Category: Bunzel, A]]	+	[[Category: Bunzel A]]
-	[[Category: Cohen~~, A E~~]]	+	[[Category: Cohen AE]]
-	[[Category: Hilvert, D]]	+	[[Category: Hilvert D]]
-	[[Category: Kern, D]]	+	[[Category: Kern D]]
-	[[Category: Nguyen, V]]	+	[[Category: Nguyen V]]
-	[[Category: Otten, R]]	+	[[Category: Otten R]]
-	[[Category: Padua~~, R A.P~~]]	+	[[Category: Padua RAP]]
-	[[Category: Patterson, M]]	+	[[Category: Patterson M]]
-	[[Category: Perry~~, S L~~]]	+	[[Category: Perry SL]]
-	[[Category: Pitsawong, W]]	+	[[Category: Pitsawong W]]
-	[[Category: Sui, S]]	+	[[Category: Sui S]]
-	~~[[Category: Directed evolution]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Kemp elimination~~]]	+

OCA at 07:06, 30 December 2020

OCA — Wed, 30 Dec 2020 07:06:27 GMT

←Older revision		Revision as of 07:06, 30 December 2020
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	==Crystal structure of Kemp Eliminase HG3.7==		==Crystal structure of Kemp Eliminase HG3.7==
-	<StructureSection load='7k4s' size='340' side='right'caption='[[7k4s]]' scene=''>	+	<StructureSection load='7k4s' size='340' side='right'caption='[[7k4s]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7K4S OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7K4S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7k4s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Theau Theau]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7K4S OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7K4S FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7k4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k4s OCA], [http://pdbe.org/7k4s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7k4s RCSB], [http://www.ebi.ac.uk/pdbsum/7k4s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7k4s ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">XYNA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5087 THEAU])</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://proteopedia.org/fgij/fg.htm?mol=7k4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k4s OCA], [http://pdbe.org/7k4s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7k4s RCSB], [http://www.ebi.ac.uk/pdbsum/7k4s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7k4s ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The advent of biocatalysts designed computationally and optimized by laboratory evolution provides an opportunity to explore molecular strategies for augmenting catalytic function. Applying a suite of nuclear magnetic resonance, crystallography, and stopped-flow techniques to an enzyme designed for an elementary proton transfer reaction, we show how directed evolution gradually altered the conformational ensemble of the protein scaffold to populate a narrow, highly active conformational ensemble and accelerate this transformation by nearly nine orders of magnitude. Mutations acquired during optimization enabled global conformational changes, including high-energy backbone rearrangements, that cooperatively organized the catalytic base and oxyanion stabilizer, thus perfecting transition-state stabilization. The development of protein catalysts for many chemical transformations could be facilitated by explicitly sampling conformational substates during design and specifically stabilizing productive substates over all unproductive conformations.
		+
		+	How directed evolution reshapes the energy landscape in an enzyme to boost catalysis.,Otten R, Padua RAP, Bunzel HA, Nguyen V, Pitsawong W, Patterson M, Sui S, Perry SL, Cohen AE, Hilvert D, Kern D Science. 2020 Dec 18;370(6523):1442-1446. doi: 10.1126/science.abd3623. Epub 2020, Nov 19. PMID:33214289<ref>PMID:33214289</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7k4s" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bunzel A]]	+	[[Category: Theau]]
-	[[Category: Cohen AE]]	+	[[Category: Bunzel, A]]
-	[[Category: Hilvert D]]	+	[[Category: Cohen, A E]]
-	[[Category: Kern D]]	+	[[Category: Hilvert, D]]
-	[[Category: Nguyen V]]	+	[[Category: Kern, D]]
-	[[Category: Otten R]]	+	[[Category: Nguyen, V]]
-	[[Category: Padua ~~RAP~~]]	+	[[Category: Otten, R]]
-	[[Category: Patterson M]]	+	[[Category: Padua, R A.P]]
-	[[Category: Perry SL]]	+	[[Category: Patterson, M]]
-	[[Category: Pitsawong W]]	+	[[Category: Perry, S L]]
-	[[Category: Sui S]]	+	[[Category: Pitsawong, W]]
		+	[[Category: Sui, S]]
		+	[[Category: Directed evolution]]
		+	[[Category: Hydrolase]]
		+	[[Category: Kemp elimination]]

OCA at 07:56, 2 December 2020

OCA — Wed, 02 Dec 2020 07:56:24 GMT

←Older revision		Revision as of 07:56, 2 December 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 7k4s is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Kemp Eliminase HG3.7==
-		+	<StructureSection load='7k4s' size='340' side='right'caption='[[7k4s]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7K4S OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7K4S FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7k4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k4s OCA], [http://pdbe.org/7k4s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7k4s RCSB], [http://www.ebi.ac.uk/pdbsum/7k4s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7k4s ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bunzel A]]
		+	[[Category: Cohen AE]]
		+	[[Category: Hilvert D]]
		+	[[Category: Kern D]]
		+	[[Category: Nguyen V]]
		+	[[Category: Otten R]]
		+	[[Category: Padua RAP]]
		+	[[Category: Patterson M]]
		+	[[Category: Perry SL]]
		+	[[Category: Pitsawong W]]
		+	[[Category: Sui S]]

OCA at 06:49, 21 October 2020

OCA — Wed, 21 Oct 2020 06:49:35 GMT

←Older revision		Revision as of 06:49, 21 October 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7k4s is ON HOLD	+	The entry 7k4s is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7k4s" [edit=sysop:move=sysop]

OCA — Wed, 23 Sep 2020 09:14:31 GMT

Protected "7k4s" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:14, 23 September 2020

OCA: New page: '''Unreleased structure''' The entry 7k4s is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 23 Sep 2020 09:14:29 GMT

New page: '''Unreleased structure''' The entry 7k4s is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7k4s is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]