7di1 - Revision history

OCA at 16:33, 29 November 2023

OCA — Wed, 29 Nov 2023 16:33:52 GMT

←Older revision		Revision as of 16:33, 29 November 2023
Line 3:		Line 3:
	<StructureSection load='7di1' size='340' side='right'caption='[[7di1]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='7di1' size='340' side='right'caption='[[7di1]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7di1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DI1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7di1]] 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=7DI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DI1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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]] 2.097Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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=7di1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7di1 OCA], [https://pdbe.org/7di1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7di1 RCSB], [https://www.ebi.ac.uk/pdbsum/7di1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7di1 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=7di1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7di1 OCA], [https://pdbe.org/7di1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7di1 RCSB], [https://www.ebi.ac.uk/pdbsum/7di1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7di1 ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Tagami, S~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Yagi,~~ S]]	+	[[Category: Tagami S]]
-	[[Category: ~~Chaperone]]~~	+	[[Category: Yagi S]]
-	~~[[Category: Double psi beta barrel~~]]	+

OCA at 14:11, 17 November 2021

OCA — Wed, 17 Nov 2021 14:11:22 GMT

←Older revision		Revision as of 14:11, 17 November 2021
Line 1:		Line 1:

	==Crystal structure of the rationally designed mkDPBB_sym_86 protein==		==Crystal structure of the rationally designed mkDPBB_sym_86 protein==
-	<StructureSection load='7di1' size='340' side='right'caption='[[7di1]]' scene=''>	+	<StructureSection load='7di1' size='340' side='right'caption='[[7di1]], [[Resolution\|resolution]] 2.10Å' 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=7DI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DI1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7di1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DI1 FirstGlance]. <br>
-	</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=7di1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7di1 OCA], [https://pdbe.org/7di1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7di1 RCSB], [https://www.ebi.ac.uk/pdbsum/7di1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7di1 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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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=7di1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7di1 OCA], [https://pdbe.org/7di1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7di1 RCSB], [https://www.ebi.ac.uk/pdbsum/7di1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7di1 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The extant complex proteins must have evolved from ancient short and simple ancestors. The double-psi beta-barrel (DPBB) is one of the oldest protein folds and conserved in various fundamental enzymes, such as the core domain of RNA polymerase. Here, by reverse engineering a modern DPBB domain, we reconstructed its plausible evolutionary pathway started by "interlacing homodimerization" of a half-size peptide, followed by gene duplication and fusion. Furthermore, by simplifying the amino acid repertoire of the peptide, we successfully created the DPBB fold with only seven amino acid types (Ala, Asp, Glu, Gly, Lys, Arg, and Val), which can be coded by only GNN and ARR (R = A or G) codons in the modern translation system. Thus, the DPBB fold could have been materialized by the early translation system and genetic code.
		+
		+	Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase.,Yagi S, Padhi AK, Vucinic J, Barbe S, Schiex T, Nakagawa R, Simoncini D, Zhang KYJ, Tagami S J Am Chem Soc. 2021 Oct 6;143(39):15998-16006. doi: 10.1021/jacs.1c05367. Epub, 2021 Sep 24. PMID:34559526<ref>PMID:34559526</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7di1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Tagami S]]	+	[[Category: Tagami, S]]
-	[[Category: Yagi S]]	+	[[Category: Yagi, S]]
		+	[[Category: Chaperone]]
		+	[[Category: Double psi beta barrel]]

OCA at 08:48, 29 September 2021

OCA — Wed, 29 Sep 2021 08:48:10 GMT

←Older revision		Revision as of 08:48, 29 September 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7di1 ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of the rationally designed mkDPBB_sym_86 protein==
-		+	<StructureSection load='7di1' size='340' side='right'caption='[[7di1]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DI1 FirstGlance]. <br>
-	~~Description~~:	+	</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=7di1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7di1 OCA], [https://pdbe.org/7di1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7di1 RCSB], [https://www.ebi.ac.uk/pdbsum/7di1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7di1 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Tagami S]]
		+	[[Category: Yagi S]]

OCA at 13:13, 3 March 2021

OCA — Wed, 03 Mar 2021 13:13:33 GMT

←Older revision		Revision as of 13:13, 3 March 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7di1 is ON HOLD	+	The entry 7di1 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7di1" [edit=sysop:move=sysop]

OCA — Wed, 25 Nov 2020 05:24:36 GMT

Protected "7di1" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:24, 25 November 2020

OCA: New page: '''Unreleased structure''' The entry 7di1 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 25 Nov 2020 05:24:35 GMT

New page: '''Unreleased structure''' The entry 7di1 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7di1 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]