6q3u - Revision history

OCA at 11:52, 24 January 2024

OCA — Wed, 24 Jan 2024 11:52:17 GMT

←Older revision		Revision as of 11:52, 24 January 2024
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	<StructureSection load='6q3u' size='340' side='right'caption='[[6q3u]], [[Resolution\|resolution]] 1.64Å' scene=''>		<StructureSection load='6q3u' size='340' side='right'caption='[[6q3u]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6q3u]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q3U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6Q3U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6q3u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q3U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Q3U 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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.64Å</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=6q3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q3u OCA], [~~http~~://pdbe.org/6q3u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6q3u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6q3u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6q3u ProSAT]</span></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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6q3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q3u OCA], [https://pdbe.org/6q3u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6q3u RCSB], [https://www.ebi.ac.uk/pdbsum/6q3u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6q3u ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9WZ62_THEMA Q9WZ62_THEMA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6q3u" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6q3u" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[ABC transporter 3D structures\|ABC transporter 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Balasco, N]]	+	[[Category: Thermotoga maritima MSB8]]
-	[[Category: Ruggiero, A]]	+	[[Category: Balasco N]]
-	[[Category: Smaldone, G]]	+	[[Category: Ruggiero A]]
-	[[Category: Vitagliano, L]]	+	[[Category: Smaldone G]]
-	~~[[Category: Gly52ala mutation]]~~	+	[[Category: Vitagliano L]]
-	~~[[Category: Helix insertion motif]]~~	+
-	~~[[Category: Local strain]]~~	+
-	~~[[Category: Protein stability]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 11:25, 10 May 2019

OCA — Fri, 10 May 2019 11:25:16 GMT

←Older revision		Revision as of 11:25, 10 May 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6q3u is ~~ON HOLD until Paper~~ Publication	+	==Gly52Ala mutant of arginine-bound ArgBP from T. maritima==
		+	<StructureSection load='6q3u' size='340' side='right'caption='[[6q3u]], [[Resolution\|resolution]] 1.64Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6q3u]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q3U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6Q3U 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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6q3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q3u OCA], [http://pdbe.org/6q3u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6q3u RCSB], [http://www.ebi.ac.uk/pdbsum/6q3u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6q3u ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Ramachandran plot is a versatile and valuable tool that provides fundamental information for protein structure determination, prediction, and validation. The structural/thermodynamic effects produced by forcing a residue to adopt a conformation predicted to be forbidden were here explored using Thermotoga maritima Arginine Binding Protein (TmArgBP) as model. Specifically, we mutated TmArgBP Gly52 that assumes a conformation believed to be strictly disallowed for non-Gly residues. Surprisingly, the crystallographic characterization of Gly52Ala TmArgBP indicates that the structural context forces the residue to adopt a non-canonical conformation never observed in any of the high-medium resolution PDB structures. Interestingly, the inspection of this high resolution structure demonstrates that only minor alterations occur. Nevertheless, experiments indicate that Gly52 replacements in TmArgBP produce destabilizations comparable to those observed upon protein truncation or dissection in domains. Notably, we show that force-fields commonly used in computational biology do not reproduce this non-canonical state. Using TmArgBP as model system we here demonstrate that the structural context may force residues to adopt conformations believed to be strictly forbidden and that barely detectable alterations produce major destabilizations. Present findings highlight the role of subtle strains in governing protein stability. A full understanding of these phenomena is essential for an exhaustive comprehension of the factors regulating protein structures.

-	~~Authors: Balasco~~, N., Smaldone, G., Ruggiero, A., Vitagliano, L.	+	The characterization of Thermotoga maritima Arginine Binding Protein variants demonstrates that minimal local strains have an important impact on protein stability.,Balasco N, Smaldone G, Vigorita M, Del Vecchio P, Graziano G, Ruggiero A, Vitagliano L Sci Rep. 2019 Apr 29;9(1):6617. doi: 10.1038/s41598-019-43157-y. PMID:31036855<ref>PMID:31036855</ref>

-	~~Description: Gly52Ala mutant~~ of ~~arginine-bound ArgBP from T~~. ~~maritima~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6q3u" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Balasco, N]]		[[Category: Balasco, N]]
-	[[Category: Smaldone, G]]
	[[Category: Ruggiero, A]]		[[Category: Ruggiero, A]]
		+	[[Category: Smaldone, G]]
	[[Category: Vitagliano, L]]		[[Category: Vitagliano, L]]
		+	[[Category: Gly52ala mutation]]
		+	[[Category: Helix insertion motif]]
		+	[[Category: Local strain]]
		+	[[Category: Protein stability]]
		+	[[Category: Transport protein]]

OCA at 06:41, 19 December 2018

OCA — Wed, 19 Dec 2018 06:41:50 GMT

←Older revision		Revision as of 06:41, 19 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6q3u is ON HOLD	+	The entry 6q3u is ON HOLD until Paper Publication

	Authors: Balasco, N., Smaldone, G., Ruggiero, A., Vitagliano, L.		Authors: Balasco, N., Smaldone, G., Ruggiero, A., Vitagliano, L.

OCA: Protected "6q3u" [edit=sysop:move=sysop]

OCA — Wed, 12 Dec 2018 05:32:15 GMT

Protected "6q3u" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:32, 12 December 2018

OCA: New page: '''Unreleased structure''' The entry 6q3u is ON HOLD Authors: Balasco, N., Smaldone, G., Ruggiero, A., Vitagliano, L. Description: Gly52Ala mutant of arginine-bound ArgBP from T. marit...

OCA — Wed, 12 Dec 2018 05:32:14 GMT

New page: '''Unreleased structure''' The entry 6q3u is ON HOLD Authors: Balasco, N., Smaldone, G., Ruggiero, A., Vitagliano, L. Description: Gly52Ala mutant of arginine-bound ArgBP from T. marit...

New page

'''Unreleased structure'''

The entry 6q3u is ON HOLD

Authors: Balasco, N., Smaldone, G., Ruggiero, A., Vitagliano, L.

Description: Gly52Ala mutant of arginine-bound ArgBP from T. maritima
[[Category: Unreleased Structures]]
[[Category: Balasco, N]]
[[Category: Smaldone, G]]
[[Category: Ruggiero, A]]
[[Category: Vitagliano, L]]