4d8h - Revision history

OCA at 10:42, 1 March 2024

2024-03-01T10:42:38Z

←Older revision		Revision as of 10:42, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4d8h]] 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=4D8H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D8H FirstGlance]. <br>		<table><tr><td colspan='2'>[[4d8h]] 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=4D8H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D8H 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>, <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]] 1.901Å</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>, <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=4d8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d8h OCA], [https://pdbe.org/4d8h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d8h RCSB], [https://www.ebi.ac.uk/pdbsum/4d8h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d8h 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=4d8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d8h OCA], [https://pdbe.org/4d8h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d8h RCSB], [https://www.ebi.ac.uk/pdbsum/4d8h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d8h ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A compendium of different types of abiotic chemical syntheses identifies a consensus set of 10 "prebiotic" alpha-amino acids. Before the emergence of biosynthetic pathways, this set is the most plausible resource for protein formation (i.e., proteogenesis) within the overall process of abiogenesis. An essential unsolved question regarding this prebiotic set is whether it defines a "foldable set"-that is, does it contain sufficient chemical information to permit cooperatively folding polypeptides? If so, what (if any) characteristic properties might such polypeptides exhibit? To investigate these questions, two "primitive" versions of an extant protein fold (the beta-trefoil) were produced by top-down symmetric deconstruction, resulting in a reduced alphabet size of 12 or 13 amino acids and a percentage of prebiotic amino acids approaching 80%. These proteins show a substantial acidification of pI and require high salt concentrations for cooperative folding. The results suggest that the prebiotic amino acids do comprise a foldable set within the halophile environment.
-
-	Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein.,M Longo L, Lee J, Blaber M Proc Natl Acad Sci U S A. 2013 Jan 22. PMID:23341608<ref>PMID:23341608</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4d8h" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:52, 14 September 2022

2022-09-14T07:52:31Z

←Older revision		Revision as of 07:52, 14 September 2022
Line 3:		Line 3:
	<StructureSection load='4d8h' size='340' side='right'caption='[[4d8h]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4d8h' size='340' side='right'caption='[[4d8h]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4d8h]] 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=4D8H OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4D8H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4d8h]] 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=4D8H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D8H FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jqz\|1jqz]]~~</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=4d8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d8h OCA], [https://pdbe.org/4d8h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d8h RCSB], [https://www.ebi.ac.uk/pdbsum/4d8h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d8h 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=4d8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d8h OCA], [~~http~~://pdbe.org/4d8h PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4d8h RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4d8h PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4d8h ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Blaber, M]]	+	[[Category: Blaber M]]
-	[[Category: Longo, L]]	+	[[Category: Longo L]]
-	~~[[Category: Beta-trefoil]]~~	+
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: Pre-biotic]]~~	+
-	~~[[Category: Symfoil]]~~	+
-	~~[[Category: Symmetric~~]]	+

OCA at 08:16, 27 March 2019

2019-03-27T08:16:23Z

←Older revision		Revision as of 08:16, 27 March 2019
Line 1:		Line 1:

	==Crystal structure of Symfoil-4P/PV2: de novo designed beta-trefoil architecture with symmetric primary structure, primitive version 2 (6xLeu / PV1)==		==Crystal structure of Symfoil-4P/PV2: de novo designed beta-trefoil architecture with symmetric primary structure, primitive version 2 (6xLeu / PV1)==
-	<StructureSection load='4d8h' size='340' side='right' caption='[[4d8h]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='4d8h' size='340' side='right'caption='[[4d8h]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4d8h]] 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=4D8H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D8H FirstGlance]. <br>		<table><tr><td colspan='2'>[[4d8h]] 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=4D8H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D8H FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Synthetic construct sequences]]		[[Category: Synthetic construct sequences]]
	[[Category: Blaber, M]]		[[Category: Blaber, M]]

OCA at 22:02, 5 August 2016

2016-08-05T22:02:51Z

←Older revision		Revision as of 22:02, 5 August 2016
Line 1:		Line 1:
-	{{STRUCTURE_4d8h\| PDB=4d8h \| SCENE= }}
-	===Crystal structure of Symfoil-4P/PV2: de novo designed beta-trefoil architecture with symmetric primary structure, primitive version 2 (6xLeu / PV1)===
-	{{ABSTRACT_PUBMED_23341608}}

-	==~~About this Structure~~==	+	==Crystal structure of Symfoil-4P/PV2: de novo designed beta-trefoil architecture with symmetric primary structure, primitive version 2 (6xLeu / PV1)==
-	[[4d8h]] 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=4D8H OCA].	+	<StructureSection load='4d8h' size='340' side='right' caption='[[4d8h]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4d8h]] 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=4D8H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D8H FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jqz\|1jqz]]</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=4d8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d8h OCA], [http://pdbe.org/4d8h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d8h RCSB], [http://www.ebi.ac.uk/pdbsum/4d8h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4d8h ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A compendium of different types of abiotic chemical syntheses identifies a consensus set of 10 "prebiotic" alpha-amino acids. Before the emergence of biosynthetic pathways, this set is the most plausible resource for protein formation (i.e., proteogenesis) within the overall process of abiogenesis. An essential unsolved question regarding this prebiotic set is whether it defines a "foldable set"-that is, does it contain sufficient chemical information to permit cooperatively folding polypeptides? If so, what (if any) characteristic properties might such polypeptides exhibit? To investigate these questions, two "primitive" versions of an extant protein fold (the beta-trefoil) were produced by top-down symmetric deconstruction, resulting in a reduced alphabet size of 12 or 13 amino acids and a percentage of prebiotic amino acids approaching 80%. These proteins show a substantial acidification of pI and require high salt concentrations for cooperative folding. The results suggest that the prebiotic amino acids do comprise a foldable set within the halophile environment.

-	~~==Reference==~~	+	Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein.,M Longo L, Lee J, Blaber M Proc Natl Acad Sci U S A. 2013 Jan 22. PMID:23341608<ref>PMID:23341608</ref>
-	<ref ~~group="xtra"~~>PMID:~~023341608~~</ref><~~references group~~="~~xtra~~"/><references/>	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4d8h" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Synthetic construct sequences]]		[[Category: Synthetic construct sequences]]
-	[[Category: Blaber, M.]]	+	[[Category: Blaber, M]]
-	[[Category: Longo, L.]]	+	[[Category: Longo, L]]
	[[Category: Beta-trefoil]]		[[Category: Beta-trefoil]]
	[[Category: De novo protein]]		[[Category: De novo protein]]

OCA at 08:18, 18 December 2013

2013-12-18T08:18:11Z

←Older revision		Revision as of 08:18, 18 December 2013
Line 1:		Line 1:
	{{STRUCTURE_4d8h\| PDB=4d8h \| SCENE= }}		{{STRUCTURE_4d8h\| PDB=4d8h \| SCENE= }}
-	===Crystal structure of ~~F22L/F44L/F64L/F85L/F108L/F132L hisSymfoil~~-4P/~~PV1 (6xLeu PV1)~~ de novo designed beta-trefoil ~~enriched for pre-biotic amino acids~~===	+	===Crystal structure of Symfoil-4P/PV2: de novo designed beta-trefoil architecture with symmetric primary structure, primitive version 2 (6xLeu / PV1)===
	{{ABSTRACT_PUBMED_23341608}}		{{ABSTRACT_PUBMED_23341608}}

	==About this Structure==		==About this Structure==
-	[[4d8h]] is a 1 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=4D8H OCA].	+	[[4d8h]] 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=4D8H OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:023341608</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:023341608</ref><references group="xtra"/><references/>
-	[[Category: Synthetic construct]]	+	[[Category: Synthetic construct sequences]]
	[[Category: Blaber, M.]]		[[Category: Blaber, M.]]
	[[Category: Longo, L.]]		[[Category: Longo, L.]]

OCA at 06:33, 20 June 2013

2013-06-20T06:33:09Z

←Older revision		Revision as of 06:33, 20 June 2013
Line 1:		Line 1:
-	[[Image:4d8h.png\|left\|200px]]
-
	{{STRUCTURE_4d8h\| PDB=4d8h \| SCENE= }}		{{STRUCTURE_4d8h\| PDB=4d8h \| SCENE= }}
-
	===Crystal structure of F22L/F44L/F64L/F85L/F108L/F132L hisSymfoil-4P/PV1 (6xLeu PV1) de novo designed beta-trefoil enriched for pre-biotic amino acids===		===Crystal structure of F22L/F44L/F64L/F85L/F108L/F132L hisSymfoil-4P/PV1 (6xLeu PV1) de novo designed beta-trefoil enriched for pre-biotic amino acids===
-
	{{ABSTRACT_PUBMED_23341608}}		{{ABSTRACT_PUBMED_23341608}}

	==About this Structure==		==About this Structure==
	[[4d8h]] is a 1 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=4D8H OCA].		[[4d8h]] is a 1 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=4D8H OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023341608</ref><references group="xtra"/><references/>
	[[Category: Synthetic construct]]		[[Category: Synthetic construct]]
	[[Category: Blaber, M.]]		[[Category: Blaber, M.]]

OCA at 12:55, 6 February 2013

2013-02-06T12:55:20Z

←Older revision		Revision as of 12:55, 6 February 2013
Line 1:		Line 1:
-	[[Image:4d8h.~~jpg~~\|left\|200px]]	+	[[Image:4d8h.png\|left\|200px]]

	{{STRUCTURE_4d8h\| PDB=4d8h \| SCENE= }}		{{STRUCTURE_4d8h\| PDB=4d8h \| SCENE= }}
Line 5:		Line 5:
	===Crystal structure of F22L/F44L/F64L/F85L/F108L/F132L hisSymfoil-4P/PV1 (6xLeu PV1) de novo designed beta-trefoil enriched for pre-biotic amino acids===		===Crystal structure of F22L/F44L/F64L/F85L/F108L/F132L hisSymfoil-4P/PV1 (6xLeu PV1) de novo designed beta-trefoil enriched for pre-biotic amino acids===

		+	{{ABSTRACT_PUBMED_23341608}}

	==About this Structure==		==About this Structure==

OCA at 09:08, 16 January 2013

2013-01-16T09:08:29Z

←Older revision		Revision as of 09:08, 16 January 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4d8h.jpg\|left\|200px]]

-	~~The entry~~ 4d8h ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4d8h\| PDB=4d8h \| SCENE= }}

-	~~Authors: Blaber, M., Longo, L.~~	+	===Crystal structure of F22L/F44L/F64L/F85L/F108L/F132L hisSymfoil-4P/PV1 (6xLeu PV1) de novo designed beta-trefoil enriched for pre-biotic amino acids===

-	~~Description: Crystal~~ structure ~~of F22L~~/~~F44L~~/~~F64L~~/~~F85L~~/~~F108L~~/~~F132L hisSymfoil~~-4P/~~PV1 (6xLeu PV1) de novo designed beta~~-trefoil ~~enriched for pre~~-biotic ~~amino acids~~	+
		+	==About this Structure==
		+	[[4d8h]] is a 1 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=4D8H OCA].
		+	[[Category: Synthetic construct]]
		+	[[Category: Blaber, M.]]
		+	[[Category: Longo, L.]]
		+	[[Category: Beta-trefoil]]
		+	[[Category: De novo protein]]
		+	[[Category: Pre-biotic]]
		+	[[Category: Symfoil]]
		+	[[Category: Symmetric]]

OCA at 06:19, 15 February 2012

2012-02-15T06:19:17Z

←Older revision		Revision as of 06:19, 15 February 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4d8h is ON HOLD	+	The entry 4d8h is ON HOLD until Paper Publication

	Authors: Blaber, M., Longo, L.		Authors: Blaber, M., Longo, L.

	Description: Crystal structure of F22L/F44L/F64L/F85L/F108L/F132L hisSymfoil-4P/PV1 (6xLeu PV1) de novo designed beta-trefoil enriched for pre-biotic amino acids		Description: Crystal structure of F22L/F44L/F64L/F85L/F108L/F132L hisSymfoil-4P/PV1 (6xLeu PV1) de novo designed beta-trefoil enriched for pre-biotic amino acids

OCA: Protected "4d8h" [edit=sysop:move=sysop]

2012-01-18T10:26:38Z

Protected "4d8h" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:26, 18 January 2012