4zv1 - Revision history

OCA at 08:24, 27 September 2023

OCA — Wed, 27 Sep 2023 08:24:45 GMT

←Older revision		Revision as of 08:24, 27 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4zv1]] is a 1 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=4ZV1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZV1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4zv1]] is a 1 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=4ZV1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZV1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARG:ARGININE'>ARG</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]] 1.52Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARG:ARGININE'>ARG</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=4zv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zv1 OCA], [https://pdbe.org/4zv1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zv1 RCSB], [https://www.ebi.ac.uk/pdbsum/4zv1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zv1 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=4zv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zv1 OCA], [https://pdbe.org/4zv1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zv1 RCSB], [https://www.ebi.ac.uk/pdbsum/4zv1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zv1 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:42, 18 May 2023

OCA — Thu, 18 May 2023 07:42:45 GMT

←Older revision		Revision as of 07:42, 18 May 2023
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	<StructureSection load='4zv1' size='340' side='right'caption='[[4zv1]], [[Resolution\|resolution]] 1.52Å' scene=''>		<StructureSection load='4zv1' size='340' side='right'caption='[[4zv1]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4zv1]] is a 1 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=4ZV1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4ZV1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4zv1]] is a 1 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=4ZV1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZV1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zv2\|4zv2]]~~</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=4zv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zv1 OCA], [https://pdbe.org/4zv1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zv1 RCSB], [https://www.ebi.ac.uk/pdbsum/4zv1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zv1 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=4zv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zv1 OCA], [~~http~~://pdbe.org/4zv1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4zv1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4zv1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4zv1 ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Carr~~, P D~~]]	+	[[Category: Carr PD]]
-	[[Category: Clifton~~, B E~~]]	+	[[Category: Clifton BE]]
-	[[Category: Jackson~~, C J]]~~	+	[[Category: Jackson CJ]]
-	~~[[Category: Amino acid]]~~	+
-	~~[[Category: Periplasmic binding protein]]~~	+
-	~~[[Category: Solute binding protein]]~~	+
-	~~[[Category: Solute-binding protein]]~~	+
-	~~[[Category: Transport~~]]	+

OCA at 07:58, 26 June 2019

OCA — Wed, 26 Jun 2019 07:58:11 GMT

←Older revision		Revision as of 07:58, 26 June 2019
Line 1:		Line 1:

	==An ancestral arginine-binding protein bound to arginine==		==An ancestral arginine-binding protein bound to arginine==
-	<StructureSection load='4zv1' size='340' side='right' caption='[[4zv1]], [[Resolution\|resolution]] 1.52Å' scene=''>	+	<StructureSection load='4zv1' size='340' side='right'caption='[[4zv1]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4zv1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZV1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZV1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4zv1]] is a 1 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=4ZV1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZV1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zv2\|4zv2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zv2\|4zv2]]</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=4zv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zv1 OCA], [http://pdbe.org/4zv1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zv1 RCSB], [http://www.ebi.ac.uk/pdbsum/4zv1 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=4zv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zv1 OCA], [http://pdbe.org/4zv1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zv1 RCSB], [http://www.ebi.ac.uk/pdbsum/4zv1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zv1 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Synthetic construct sequences]]
	[[Category: Carr, P D]]		[[Category: Carr, P D]]
	[[Category: Clifton, B E]]		[[Category: Clifton, B E]]

OCA at 06:52, 2 March 2016

OCA — Wed, 02 Mar 2016 06:52:49 GMT

←Older revision		Revision as of 06:52, 2 March 2016
Line 1:		Line 1:
		+
	==An ancestral arginine-binding protein bound to arginine==		==An ancestral arginine-binding protein bound to arginine==
	<StructureSection load='4zv1' size='340' side='right' caption='[[4zv1]], [[Resolution\|resolution]] 1.52Å' scene=''>		<StructureSection load='4zv1' size='340' side='right' caption='[[4zv1]], [[Resolution\|resolution]] 1.52Å' scene=''>
Line 7:		Line 8:
	<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=4zv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zv1 OCA], [http://pdbe.org/4zv1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zv1 RCSB], [http://www.ebi.ac.uk/pdbsum/4zv1 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=4zv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zv1 OCA], [http://pdbe.org/4zv1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zv1 RCSB], [http://www.ebi.ac.uk/pdbsum/4zv1 PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The promiscuous functions of proteins are an important reservoir of functional novelty in protein evolution, but the molecular basis for binding promiscuity remains elusive. We used ancestral protein reconstruction to experimentally characterize evolutionary intermediates in the functional expansion of the polar amino acid-binding protein family, which has evolved to bind a variety of amino acids with high affinity and specificity. High-resolution crystal structures of an ancestral arginine-binding protein in complex with l-arginine and l-glutamine show that the promiscuous binding of l-glutamine is enabled by multi-scale conformational plasticity, water-mediated interactions, and selection of an alternative conformational substate productive for l-glutamine binding. Evolution of specialized glutamine-binding proteins from this ancestral protein was achieved by displacement of water molecules from the protein-ligand interface, reducing the entropic penalty associated with the promiscuous interaction. These results provide a structural and thermodynamic basis for the co-option of a promiscuous interaction in the evolution of binding specificity.
		+
		+	Ancestral Protein Reconstruction Yields Insights into Adaptive Evolution of Binding Specificity in Solute-Binding Proteins.,Clifton BE, Jackson CJ Cell Chem Biol. 2016 Feb 2. pii: S2451-9456(16)00031-3. doi:, 10.1016/j.chembiol.2015.12.010. PMID:26853627<ref>PMID:26853627</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4zv1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 15:51, 3 February 2016

OCA — Wed, 03 Feb 2016 15:51:52 GMT

←Older revision		Revision as of 15:51, 3 February 2016
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==An ancestral arginine-binding protein bound to arginine==
-		+	<StructureSection load='4zv1' size='340' side='right' caption='[[4zv1]], [[Resolution\|resolution]] 1.52Å' scene=''>
-	~~The entry~~ 4zv1 is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4zv1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZV1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZV1 FirstGlance]. <br>
-	~~Authors~~: ~~Clifton~~, B.E., ~~Carr~~, P.D., ~~Jackson, C~~.J.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zv2\|4zv2]]</td></tr>
-	~~Description~~: ~~An ancestral arginine-binding protein bound to arginine~~	+	<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=4zv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zv1 OCA], [http://pdbe.org/4zv1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zv1 RCSB], [http://www.ebi.ac.uk/pdbsum/4zv1 PDBsum]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: Jackson, C.J]]	+	__TOC__
-	[[Category: ~~Clifton, B.E~~]]	+	</StructureSection>
-	[[Category: ~~Carr, P.D~~]]	+	[[Category: Carr, P D]]
		+	[[Category: Clifton, B E]]
		+	[[Category: Jackson, C J]]
		+	[[Category: Amino acid]]
		+	[[Category: Periplasmic binding protein]]
		+	[[Category: Solute binding protein]]
		+	[[Category: Solute-binding protein]]
		+	[[Category: Transport]]

OCA at 11:13, 3 June 2015

OCA — Wed, 03 Jun 2015 11:13:57 GMT

←Older revision		Revision as of 11:13, 3 June 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4zv1 is ON HOLD	+	The entry 4zv1 is ON HOLD until Paper Publication

	Authors: Clifton, B.E., Carr, P.D., Jackson, C.J.		Authors: Clifton, B.E., Carr, P.D., Jackson, C.J.

OCA: Protected "4zv1" [edit=sysop:move=sysop]

OCA — Wed, 27 May 2015 14:45:15 GMT

Protected "4zv1" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:45, 27 May 2015

OCA: New page: '''Unreleased structure''' The entry 4zv1 is ON HOLD Authors: Clifton, B.E., Carr, P.D., Jackson, C.J. Description: An ancestral arginine-binding protein bound to arginine [[Category: ...

OCA — Wed, 27 May 2015 14:45:14 GMT

New page: '''Unreleased structure''' The entry 4zv1 is ON HOLD Authors: Clifton, B.E., Carr, P.D., Jackson, C.J. Description: An ancestral arginine-binding protein bound to arginine [[Category: ...

New page

'''Unreleased structure'''

The entry 4zv1 is ON HOLD

Authors: Clifton, B.E., Carr, P.D., Jackson, C.J.

Description: An ancestral arginine-binding protein bound to arginine
[[Category: Unreleased Structures]]
[[Category: Jackson, C.J]]
[[Category: Clifton, B.E]]
[[Category: Carr, P.D]]