4gy1 - Revision history

OCA at 07:25, 26 October 2022

OCA — Wed, 26 Oct 2022 07:25:25 GMT

←Older revision		Revision as of 07:25, 26 October 2022
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	<StructureSection load='4gy1' size='340' side='right'caption='[[4gy1]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='4gy1' size='340' side='right'caption='[[4gy1]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4gy1]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GY1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4GY1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4gy1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GY1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GY1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</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=4gy1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gy1 OCA], [https://pdbe.org/4gy1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gy1 RCSB], [https://www.ebi.ac.uk/pdbsum/4gy1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gy1 ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e3t\|4e3t]]~~, ~~[[4gy0\|4gy0]]~~<~~/td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Aryldialkylphosphatase Aryldialkylphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.1 3.1.8.1]~~ </~~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=4gy1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gy1 OCA], [~~http~~://pdbe.org/4gy1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4gy1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4gy1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4gy1 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/OPD_BREDI OPD_BREDI] Has an unusual substrate specificity for synthetic organophosphate triesters and phosphorofluoridates. All of the phosphate triesters found to be substrates are synthetic compounds. The identity of any naturally occurring substrate for the enzyme is unknown. Has no detectable activity with phosphate monoesters or diesters and no activity as an esterase or protease. It catalyzes the hydrolysis of the insecticide paraoxon at a rate approaching the diffusion limit and thus appears to be optimally evolved for utilizing this synthetic substrate.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Phosphotriesterase\|Phosphotriesterase]]	+	*[[Phosphotriesterase 3D structures\|Phosphotriesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Aryldialkylphosphatase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Jackson~~, C J~~]]	+	[[Category: Jackson CJ]]
-	[[Category: Tawfik~~, D S~~]]	+	[[Category: Tawfik DS]]
-	[[Category: Tokuriki, N]]	+	[[Category: Tokuriki N]]
-	~~[[Category: Alpha/beta hydrolase]]~~	+
-	~~[[Category: Arylesterase]]~~	+
-	~~[[Category: Carboxylated lysine]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:19, 27 March 2019

OCA — Wed, 27 Mar 2019 07:19:55 GMT

←Older revision		Revision as of 07:19, 27 March 2019
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	==Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate==		==Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate==
-	<StructureSection load='4gy1' size='340' side='right' caption='[[4gy1]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='4gy1' size='340' side='right'caption='[[4gy1]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4gy1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GY1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GY1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4gy1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GY1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GY1 FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Aryldialkylphosphatase]]		[[Category: Aryldialkylphosphatase]]
		+	[[Category: Large Structures]]
	[[Category: Synthetic construct sequences]]		[[Category: Synthetic construct sequences]]
	[[Category: Jackson, C J]]		[[Category: Jackson, C J]]

OCA at 08:28, 4 August 2016

OCA — Thu, 04 Aug 2016 08:28:35 GMT

←Older revision		Revision as of 08:28, 4 August 2016
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		+
	==Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate==		==Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate==
	<StructureSection load='4gy1' size='340' side='right' caption='[[4gy1]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='4gy1' size='340' side='right' caption='[[4gy1]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4gy1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Synthetic_construct~~ Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GY1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GY1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4gy1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GY1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GY1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e3t\|4e3t]], [[4gy0\|4gy0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e3t\|4e3t]], [[4gy0\|4gy0]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aryldialkylphosphatase Aryldialkylphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.1 3.1.8.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aryldialkylphosphatase Aryldialkylphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.1 3.1.8.1] </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=4gy1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gy1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gy1 RCSB], [http://www.ebi.ac.uk/pdbsum/4gy1 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=4gy1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gy1 OCA], [http://pdbe.org/4gy1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gy1 RCSB], [http://www.ebi.ac.uk/pdbsum/4gy1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gy1 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 4gy1" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 25:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Aryldialkylphosphatase]]		[[Category: Aryldialkylphosphatase]]
-	[[Category: Synthetic construct]]	+	[[Category: Synthetic construct sequences]]
	[[Category: Jackson, C J]]		[[Category: Jackson, C J]]
	[[Category: Tawfik, D S]]		[[Category: Tawfik, D S]]

OCA at 10:41, 21 December 2014

OCA — Sun, 21 Dec 2014 10:41:18 GMT

←Older revision		Revision as of 10:41, 21 December 2014
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-	~~{{STRUCTURE_4gy1\| PDB=4gy1 \| SCENE= }}~~	+	==Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate==
-	===Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate===	+	<StructureSection load='4gy1' size='340' side='right' caption='[[4gy1]], [[Resolution\|resolution]] 1.50Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23212386}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4gy1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GY1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GY1 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e3t\|4e3t]], [[4gy0\|4gy0]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aryldialkylphosphatase Aryldialkylphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.1 3.1.8.1] </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=4gy1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gy1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gy1 RCSB], [http://www.ebi.ac.uk/pdbsum/4gy1 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Optimization processes, such as evolution, are constrained by diminishing returns-the closer the optimum, the smaller the benefit per mutation, and by tradeoffs-improvement of one property at the cost of others. However, the magnitude and molecular basis of these parameters, and their effect on evolutionary transitions, remain unknown. Here we pursue a complete functional transition of an enzyme with a >10(9)-fold change in the enzyme's selectivity using laboratory evolution. We observed strong diminishing returns, with the initial mutations conferring >25-fold higher improvements than later ones, and asymmetric tradeoffs whereby the gain/loss ratio of the new/old activity decreased 400-fold from the beginning of the trajectory to its end. We describe the molecular basis for these phenomena and suggest they have an important role in shaping natural proteins. These findings also suggest that the catalytic efficiency and specificity of many natural enzymes may be far from their optimum.

-	~~==About this Structure==~~	+	Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme.,Tokuriki N, Jackson CJ, Afriat-Jurnou L, Wyganowski KT, Tang R, Tawfik DS Nat Commun. 2012 Dec 4;3:1257. doi: 10.1038/ncomms2246. PMID:23212386<ref>PMID:23212386</ref>
-	~~[[4gy1]] is a 2 chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org~~/~~wiki/Synthetic_construct Synthetic construct]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4GY1 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group~~=~~"xtra">PMID:023212386</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+
		+	==See Also==
		+	*[[Phosphotriesterase\|Phosphotriesterase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Aryldialkylphosphatase]]		[[Category: Aryldialkylphosphatase]]
	[[Category: Synthetic construct]]		[[Category: Synthetic construct]]
-	[[Category: Jackson, C J.]]	+	[[Category: Jackson, C J]]
-	[[Category: Tawfik, D S.]]	+	[[Category: Tawfik, D S]]
-	[[Category: Tokuriki, N.]]	+	[[Category: Tokuriki, N]]
	[[Category: Alpha/beta hydrolase]]		[[Category: Alpha/beta hydrolase]]
	[[Category: Arylesterase]]		[[Category: Arylesterase]]
	[[Category: Carboxylated lysine]]		[[Category: Carboxylated lysine]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 08:20, 21 August 2013

OCA — Wed, 21 Aug 2013 08:20:29 GMT

←Older revision		Revision as of 08:20, 21 August 2013
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-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4gy1\| PDB=4gy1 \| SCENE= }}
		+	===Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate===
		+	{{ABSTRACT_PUBMED_23212386}}

-	~~The entry~~ 4gy1 is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4gy1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GY1 OCA].

-	~~Authors~~: Jackson, C.J.~~, Tokuriki, N.,~~ Tawfik, D.S.	+	==Reference==
-		+	<ref group="xtra">PMID:023212386</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Round 18~~ Arylesterase ~~Variant of Phosphotriesterase with Bound Cacodylate~~	+	[[Category: Aryldialkylphosphatase]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Jackson, C J.]]
		+	[[Category: Tawfik, D S.]]
		+	[[Category: Tokuriki, N.]]
		+	[[Category: Alpha/beta hydrolase]]
		+	[[Category: Arylesterase]]
		+	[[Category: Carboxylated lysine]]
		+	[[Category: Hydrolase]]

OCA at 08:36, 31 October 2012

OCA — Wed, 31 Oct 2012 08:36:08 GMT

←Older revision		Revision as of 08:36, 31 October 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4gy1 is ON HOLD	+	The entry 4gy1 is ON HOLD until Paper Publication

	Authors: Jackson, C.J., Tokuriki, N., Tawfik, D.S.		Authors: Jackson, C.J., Tokuriki, N., Tawfik, D.S.

	Description: Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate		Description: Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate

OCA at 06:55, 19 September 2012

OCA — Wed, 19 Sep 2012 06:55:45 GMT

←Older revision		Revision as of 06:55, 19 September 2012
Line 3:		Line 3:
	The entry 4gy1 is ON HOLD		The entry 4gy1 is ON HOLD

-	Authors: Jackson, C. J., Tokuriki, N., Tawfik, D. S.	+	Authors: Jackson, C.J., Tokuriki, N., Tawfik, D.S.

	Description: Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate		Description: Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate

OCA: Protected "4gy1" [edit=sysop:move=sysop]

OCA — Wed, 12 Sep 2012 04:56:14 GMT

Protected "4gy1" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:56, 12 September 2012

OCA: New page: '''Unreleased structure''' The entry 4gy1 is ON HOLD Authors: Jackson, C. J., Tokuriki, N., Tawfik, D. S. Description: Round 18 Arylesterase Variant of Phosphotriesterase with Bound Ca...

OCA — Wed, 12 Sep 2012 04:56:13 GMT

New page: '''Unreleased structure''' The entry 4gy1 is ON HOLD Authors: Jackson, C. J., Tokuriki, N., Tawfik, D. S. Description: Round 18 Arylesterase Variant of Phosphotriesterase with Bound Ca...

New page

'''Unreleased structure'''

The entry 4gy1 is ON HOLD

Authors: Jackson, C. J., Tokuriki, N., Tawfik, D. S.

Description: Round 18 Arylesterase Variant of Phosphotriesterase with Bound Cacodylate