5j3i - Revision history

OCA at 10:11, 14 June 2023

OCA — Wed, 14 Jun 2023 10:11:11 GMT

←Older revision		Revision as of 10:11, 14 June 2023
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	==NMR solution structure of [Sp, Sp]-PT dsDNA==		==NMR solution structure of [Sp, Sp]-PT dsDNA==
-	<StructureSection load='5j3i' size='340' side='right'caption='[[5j3i~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='5j3i' size='340' side='right'caption='[[5j3i]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j3i]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5J3I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j3i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_lividans Streptomyces lividans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J3I FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=GS:GUANOSINE-5-THIO-MONOPHOSPHATE'>GS</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GS:GUANOSINE-5-THIO-MONOPHOSPHATE'>GS</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5j3g\|5j3g]], [[5j3f\|5j3f]]~~</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=5j3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3i OCA], [https://pdbe.org/5j3i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j3i RCSB], [https://www.ebi.ac.uk/pdbsum/5j3i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3i ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5j3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3i OCA], [~~http~~://pdbe.org/5j3i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5j3i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5j3i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3i 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: ~~Cao, C~~]]	+	[[Category: Streptomyces lividans]]
-	[[Category: ~~Hu, Z~~]]	+	[[Category: Cao C]]
-	[[Category: ~~Lan, W~~]]	+	[[Category: Hu Z]]
-	[[Category: ~~Dna~~]]	+	[[Category: Lan W]]

OCA at 07:27, 10 June 2020

OCA — Wed, 10 Jun 2020 07:27:39 GMT

←Older revision		Revision as of 07:27, 10 June 2020
Line 1:		Line 1:

	==NMR solution structure of [Sp, Sp]-PT dsDNA==		==NMR solution structure of [Sp, Sp]-PT dsDNA==
-	<StructureSection load='5j3i' size='340' side='right' caption='[[5j3i]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='5j3i' size='340' side='right'caption='[[5j3i]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j3i]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3I OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5J3I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j3i]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5J3I FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GS:GUANOSINE-5-THIO-MONOPHOSPHATE'>GS</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GS:GUANOSINE-5-THIO-MONOPHOSPHATE'>GS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5j3g\|5j3g]], [[5j3f\|5j3f]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5j3g\|5j3g]], [[5j3f\|5j3f]]</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=5j3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3i OCA], [http://pdbe.org/5j3i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j3i RCSB], [http://www.ebi.ac.uk/pdbsum/5j3i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3i ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5j3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3i OCA], [http://pdbe.org/5j3i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j3i RCSB], [http://www.ebi.ac.uk/pdbsum/5j3i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3i 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: Cao, C]]		[[Category: Cao, C]]
	[[Category: Hu, Z]]		[[Category: Hu, Z]]
	[[Category: Lan, W]]		[[Category: Lan, W]]
	[[Category: Dna]]		[[Category: Dna]]

OCA at 03:27, 10 December 2016

OCA — Sat, 10 Dec 2016 03:27:23 GMT

←Older revision		Revision as of 03:27, 10 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5j3i is ~~ON HOLD~~	+	==NMR solution structure of [Sp, Sp]-PT dsDNA==
		+	<StructureSection load='5j3i' size='340' side='right' caption='[[5j3i]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5j3i]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J3I FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GS:GUANOSINE-5-THIO-MONOPHOSPHATE'>GS</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5j3g\|5j3g]], [[5j3f\|5j3f]]</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=5j3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3i OCA], [http://pdbe.org/5j3i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j3i RCSB], [http://www.ebi.ac.uk/pdbsum/5j3i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3i ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA phosphorothioate (PT) modification, with sulfur replacing a nonbridging phosphate oxygen in a sequence and stereo specific manner, is a novel physiological variation in bacteria. But what effects on DNA properties PT modification has is still unclear. To address this, we prepared three double-stranded (ds) DNA decamers, d(CG(PX)GCCGCCGA) with its complementary strand d(TCGGCG(PX)GCCG) (where X = O or S, i.e., PT-free dsDNA, [Sp, Sp]-PT dsDNA or [Rp, Rp]-PT dsDNA) located in gene of Streptomyces lividans. Their melting temperature (Tm) measurement indicates that [Rp, Rp]-PT dsDNA is most unstable. Their electron transfer potential detection presents an order of anti-oxidation properties: Sp-PT DNA > Rp-PT DNA > PT-free DNA. Their NMR structures demonstrate that PT modification doesn't change their B-form conformation. The sulfur in [Rp, Rp]-PT dsDNA locates in the major groove, with steric effects on protons in the sugar close to modification sites, resulting in its unstability, and facilitating its selectively interactions with ScoMcrA. We thought that PT modification was dialectical to the bacteria. It protects the hosting bacteria by working as antioxidant against H2O2, and acts as a marker, directing restriction enzyme observed in other hosts, like ScoMcrA, to correctly cleave the PT modified DNA, so that bacteria cannot spread and survive.

-	~~Authors: Lan~~, W., Hu, Z., ~~Cao~~, C.	+	Structural investigation into physiological DNA phosphorothioate modification.,Lan W, Hu Z, Shen J, Wang C, Jiang F, Liu H, Long D, Liu M, Cao C Sci Rep. 2016 May 12;6:25737. doi: 10.1038/srep25737. PMID:27169778<ref>PMID:27169778</ref>

-	~~Description: NMR solution structure of [Sp~~, ~~Sp]-PT dsDNA~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5j3i" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Cao, C]]		[[Category: Cao, C]]
-	[[Category: Lan, W]]
	[[Category: Hu, Z]]		[[Category: Hu, Z]]
		+	[[Category: Lan, W]]
		+	[[Category: Dna]]

OCA: Protected "5j3i" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 01:23:33 GMT

Protected "5j3i" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:23, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5j3i is ON HOLD Authors: Lan, W., Hu, Z., Cao, C. Description: NMR solution structure of [Sp, Sp]-PT dsDNA Category: Unreleased Structures [[Ca...

OCA — Wed, 11 May 2016 01:23:31 GMT

New page: '''Unreleased structure''' The entry 5j3i is ON HOLD Authors: Lan, W., Hu, Z., Cao, C. Description: NMR solution structure of [Sp, Sp]-PT dsDNA Category: Unreleased Structures [[Ca...

New page

'''Unreleased structure'''

The entry 5j3i is ON HOLD

Authors: Lan, W., Hu, Z., Cao, C.

Description: NMR solution structure of [Sp, Sp]-PT dsDNA
[[Category: Unreleased Structures]]
[[Category: Cao, C]]
[[Category: Lan, W]]
[[Category: Hu, Z]]