6dc1 - Revision history

OCA at 15:21, 4 October 2023

OCA — Wed, 04 Oct 2023 15:21:43 GMT

←Older revision		Revision as of 15:21, 4 October 2023
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	<StructureSection load='6dc1' size='340' side='right'caption='[[6dc1]], [[Resolution\|resolution]] 2.68Å' scene=''>		<StructureSection load='6dc1' size='340' side='right'caption='[[6dc1]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dc1]] is a 12 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=6DC1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DC1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dc1]] is a 12 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=6DC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DC1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6VP:5-NITRO-2-OXIDANYL-BENZENECARBONITRILE'>6VP</scene>, <scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 2.68Å</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=6dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dc1 OCA], [~~http~~://pdbe.org/6dc1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dc1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dc1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dc1 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6VP:5-NITRO-2-OXIDANYL-BENZENECARBONITRILE'>6VP</scene>, <scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=6dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dc1 OCA], [https://pdbe.org/6dc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dc1 RCSB], [https://www.ebi.ac.uk/pdbsum/6dc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dc1 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 24:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Carr~~, P D~~]]	+	[[Category: Carr PD]]
-	[[Category: Hong, N S]]	+	[[Category: Hong N-S]]
-	[[Category: Jackson~~, C J]]~~	+	[[Category: Jackson CJ]]
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: Directed evolution]]~~	+
-	~~[[Category: Ke07]]~~	+
-	~~[[Category: Kemp eliminase]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 04:35, 13 February 2020

OCA — Thu, 13 Feb 2020 04:35:23 GMT

←Older revision		Revision as of 04:35, 13 February 2020
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	<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=6dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dc1 OCA], [http://pdbe.org/6dc1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/6dc1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dc1 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=6dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dc1 OCA], [http://pdbe.org/6dc1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/6dc1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dc1 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Developments in computational chemistry, bioinformatics, and laboratory evolution have facilitated the de novo design and catalytic optimization of enzymes. Besides creating useful catalysts, the generation and iterative improvement of designed enzymes can provide valuable insight into the interplay between the many phenomena that have been suggested to contribute to catalysis. In this work, we follow changes in conformational sampling, electrostatic preorganization, and quantum tunneling along the evolutionary trajectory of a designed Kemp eliminase. We observe that in the Kemp Eliminase KE07, instability of the designed active site leads to the emergence of two additional active site configurations. Evolutionary conformational selection then gradually stabilizes the most efficient configuration, leading to an improved enzyme. This work exemplifies the link between conformational plasticity and evolvability and demonstrates that residues remote from the active sites of enzymes play crucial roles in controlling and shaping the active site for efficient catalysis.
		+
		+	The evolution of multiple active site configurations in a designed enzyme.,Hong NS, Petrovic D, Lee R, Gryn'ova G, Purg M, Saunders J, Bauer P, Carr PD, Lin CY, Mabbitt PD, Zhang W, Altamore T, Easton C, Coote ML, Kamerlin SCL, Jackson CJ Nat Commun. 2018 Sep 25;9(1):3900. doi: 10.1038/s41467-018-06305-y. PMID:30254369<ref>PMID:30254369</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6dc1" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Kemp eliminase\|Kemp eliminase]]		*[[Kemp eliminase\|Kemp eliminase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:31, 22 January 2020

OCA — Wed, 22 Jan 2020 16:31:06 GMT

←Older revision		Revision as of 16:31, 22 January 2020
Line 1:		Line 1:

	==Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 25 round 7==		==Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 25 round 7==
-	<StructureSection load='6dc1' size='340' side='right' caption='[[6dc1]], [[Resolution\|resolution]] 2.68Å' scene=''>	+	<StructureSection load='6dc1' size='340' side='right'caption='[[6dc1]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dc1]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DC1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dc1]] is a 12 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=6DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DC1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6VP:5-NITRO-2-OXIDANYL-BENZENECARBONITRILE'>6VP</scene>, <scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6VP:5-NITRO-2-OXIDANYL-BENZENECARBONITRILE'>6VP</scene>, <scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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=6dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dc1 OCA], [http://pdbe.org/6dc1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/6dc1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dc1 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=6dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dc1 OCA], [http://pdbe.org/6dc1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/6dc1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dc1 ProSAT]</span></td></tr>
	</table>		</table>
		+
		+	==See Also==
		+	*[[Kemp eliminase\|Kemp eliminase]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Synthetic construct sequences]]
	[[Category: Carr, P D]]		[[Category: Carr, P D]]
	[[Category: Hong, N S]]		[[Category: Hong, N S]]

OCA at 18:49, 1 August 2018

OCA — Wed, 01 Aug 2018 18:49:50 GMT

←Older revision		Revision as of 18:49, 1 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6dc1 is ~~ON HOLD~~	+	==Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 25 round 7==
-		+	<StructureSection load='6dc1' size='340' side='right' caption='[[6dc1]], [[Resolution\|resolution]] 2.68Å' scene=''>
-	~~Authors~~: ~~Jackson~~, C.J., ~~Hong~~, N.-S., ~~Carr~~, P.D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6dc1]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DC1 FirstGlance]. <br>
-	~~Description: Directed evolutionary changes in Kemp Eliminase KE07 -Crystal 25 round 7~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6VP:5-NITRO-2-OXIDANYL-BENZENECARBONITRILE'>6VP</scene>, <scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=6dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dc1 OCA], [http://pdbe.org/6dc1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/6dc1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dc1 ProSAT]</span></td></tr>
-	[[Category: Hong, N.-S]]	+	</table>
-	[[Category: Jackson, C.J]]	+	__TOC__
-	[[Category: ~~Carr, P.D~~]]	+	</StructureSection>
		+	[[Category: Carr, P D]]
		+	[[Category: Hong, N S]]
		+	[[Category: Jackson, C J]]
		+	[[Category: De novo protein]]
		+	[[Category: Directed evolution]]
		+	[[Category: Ke07]]
		+	[[Category: Kemp eliminase]]
		+	[[Category: Lyase]]

OCA at 04:15, 6 June 2018

OCA — Wed, 06 Jun 2018 04:15:34 GMT

←Older revision		Revision as of 04:15, 6 June 2018
Line 5:		Line 5:
	Authors: Jackson, C.J., Hong, N.-S., Carr, P.D.		Authors: Jackson, C.J., Hong, N.-S., Carr, P.D.

-	Description: Directed evolutionary changes in Kemp Eliminase KE07 -Crystal 27 round 7-2	+	Description: Directed evolutionary changes in Kemp Eliminase KE07 -Crystal 25 round 7
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Hong, N.-S]]		[[Category: Hong, N.-S]]
	[[Category: Jackson, C.J]]		[[Category: Jackson, C.J]]
	[[Category: Carr, P.D]]		[[Category: Carr, P.D]]

OCA: Protected "6dc1" [edit=sysop:move=sysop]

OCA — Wed, 09 May 2018 04:59:35 GMT

Protected "6dc1" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:59, 9 May 2018

OCA: New page: '''Unreleased structure''' The entry 6dc1 is ON HOLD Authors: Jackson, C.J., Hong, N.-S., Carr, P.D. Description: Directed evolutionary changes in Kemp Eliminase KE07 -Crystal 27 round...

OCA — Wed, 09 May 2018 04:59:34 GMT

New page: '''Unreleased structure''' The entry 6dc1 is ON HOLD Authors: Jackson, C.J., Hong, N.-S., Carr, P.D. Description: Directed evolutionary changes in Kemp Eliminase KE07 -Crystal 27 round...

New page

'''Unreleased structure'''

The entry 6dc1 is ON HOLD

Authors: Jackson, C.J., Hong, N.-S., Carr, P.D.

Description: Directed evolutionary changes in Kemp Eliminase KE07 -Crystal 27 round 7-2
[[Category: Unreleased Structures]]
[[Category: Hong, N.-S]]
[[Category: Jackson, C.J]]
[[Category: Carr, P.D]]