1woe - Revision history

OCA at 13:33, 13 March 2024

OCA — Wed, 13 Mar 2024 13:33:03 GMT

←Older revision		Revision as of 13:33, 13 March 2024
Line 8:		Line 8:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1woe OCA], [https://pdbe.org/1woe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1woe RCSB], [https://www.ebi.ac.uk/pdbsum/1woe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1woe 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=1woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1woe OCA], [https://pdbe.org/1woe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1woe RCSB], [https://www.ebi.ac.uk/pdbsum/1woe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1woe ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	In order to reveal the hydration structure of Z-DNA, a neutron diffraction study has been carried out at 1.8 A resolution on a Z-DNA hexamer d(CGCGCG). Neutron diffraction data were collected with the BIX-3 single-crystal diffractometer at the JRR-3 reactor in the Japan Atomic Energy Research Institute (JAERI) using a large crystal (1.6 mm3) obtained from D2O solution. It has been found that almost all the guanine bases have participated in H/D exchange at the C8-H8 group, consistent with the acidic nature of this bond. 44 water molecules were found in the nuclear density maps, of which 29 showed the entire contour of all three atoms (D-O-D). The remaining 15 water molecules had a simple spherical shape, indicating that they were rotationally disordered. An interesting relationship was found between the orientational disorder of the water molecules and their locations. Almost all water molecules in the minor groove were well ordered in the crystal, while 40% of the water molecules in the major groove were rotationally disordered. The hydrogen-bonding networks in the hydration shells have two structural aspects: flexibility and regularity.
-
-	The hydration structure of a Z-DNA hexameric duplex determined by a neutron diffraction technique.,Chatake T, Tanaka I, Umino H, Arai S, Niimura N Acta Crystallogr D Biol Crystallogr. 2005 Aug;61(Pt 8):1088-98. Epub 2005, Jul 20. PMID:16041074<ref>PMID:16041074</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1woe" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Z-DNA\|Z-DNA]]		*[[Z-DNA\|Z-DNA]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:25, 2 August 2023

OCA — Wed, 02 Aug 2023 11:25:32 GMT

←Older revision		Revision as of 11:25, 2 August 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1woe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WOE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WOE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1woe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WOE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WOE FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>~~, ~~<scene name='pdbligand=SPM:SPERMINE'>SPM</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]] 1.5Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height~~: ~~3em;~~'>~~[[1v9g\|1v9g]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</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=1woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1woe OCA], [https://pdbe.org/1woe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1woe RCSB], [https://www.ebi.ac.uk/pdbsum/1woe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1woe 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=1woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1woe OCA], [https://pdbe.org/1woe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1woe RCSB], [https://www.ebi.ac.uk/pdbsum/1woe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1woe ProSAT]</span></td></tr>
	</table>		</table>
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arai, S]]	+	[[Category: Arai S]]
-	[[Category: Chatake, T]]	+	[[Category: Chatake T]]
-	[[Category: Niimura, N]]	+	[[Category: Niimura N]]
-	[[Category: Tanaka, I]]	+	[[Category: Tanaka I]]
-	[[Category: Umino, H]]	+	[[Category: Umino H]]
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Heavy water]]~~	+
-	~~[[Category: Spermine]]~~	+
-	~~[[Category: Z-dna~~]]	+

OCA at 16:23, 27 October 2021

OCA — Wed, 27 Oct 2021 16:23:32 GMT

←Older revision		Revision as of 16:23, 27 October 2021
Line 3:		Line 3:
	<StructureSection load='1woe' size='340' side='right'caption='[[1woe]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='1woe' size='340' side='right'caption='[[1woe]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1woe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WOE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1WOE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1woe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WOE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WOE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v9g\|1v9g]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1v9g\|1v9g]]</div></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=1woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1woe OCA], [~~http~~://pdbe.org/1woe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1woe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1woe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1woe 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=1woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1woe OCA], [https://pdbe.org/1woe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1woe RCSB], [https://www.ebi.ac.uk/pdbsum/1woe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1woe ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:41, 22 January 2020

OCA — Wed, 22 Jan 2020 17:41:03 GMT

←Older revision		Revision as of 17:41, 22 January 2020
Line 1:		Line 1:

	==X-ray structure of a Z-DNA hexamer d(CGCGCG)==		==X-ray structure of a Z-DNA hexamer d(CGCGCG)==
-	<StructureSection load='1woe' size='340' side='right' caption='[[1woe]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='1woe' size='340' side='right'caption='[[1woe]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1woe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WOE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WOE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1woe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WOE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WOE FirstGlance]. <br>
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Arai, S]]		[[Category: Arai, S]]
	[[Category: Chatake, T]]		[[Category: Chatake, T]]

OCA at 16:25, 11 April 2018

OCA — Wed, 11 Apr 2018 16:25:33 GMT

←Older revision		Revision as of 16:25, 11 April 2018
Line 1:		Line 1:
		+
	==X-ray structure of a Z-DNA hexamer d(CGCGCG)==		==X-ray structure of a Z-DNA hexamer d(CGCGCG)==
	<StructureSection load='1woe' size='340' side='right' caption='[[1woe]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='1woe' size='340' side='right' caption='[[1woe]], [[Resolution\|resolution]] 1.50Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v9g\|1v9g]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v9g\|1v9g]]</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=1woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1woe OCA], [http://pdbe.org/1woe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1woe RCSB], [http://www.ebi.ac.uk/pdbsum/1woe 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=1woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1woe OCA], [http://pdbe.org/1woe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1woe RCSB], [http://www.ebi.ac.uk/pdbsum/1woe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1woe ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:11, 10 September 2015

OCA — Thu, 10 Sep 2015 11:11:50 GMT

←Older revision		Revision as of 11:11, 10 September 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v9g\|1v9g]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v9g\|1v9g]]</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=1woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1woe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1woe RCSB], [http://www.ebi.ac.uk/pdbsum/1woe 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=1woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1woe OCA], [http://pdbe.org/1woe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1woe RCSB], [http://www.ebi.ac.uk/pdbsum/1woe PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 15:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1woe" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 12:24, 18 December 2014

OCA — Thu, 18 Dec 2014 12:24:09 GMT

←Older revision		Revision as of 12:24, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1woe~~\| ~~PDB~~=1woe \| ~~SCENE~~= }}	+	==X-ray structure of a Z-DNA hexamer d(CGCGCG)==
-	===X-~~ray~~ structure of a Z-DNA hexamer d(CGCGCG)~~===~~	+	<StructureSection load='1woe' size='340' side='right' caption='[[1woe]], [[Resolution\|resolution]] 1.50Å' scene=''>
-	~~{{ABSTRACT_PUBMED_16041074}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1woe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WOE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WOE FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v9g\|1v9g]]</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=1woe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1woe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1woe RCSB], [http://www.ebi.ac.uk/pdbsum/1woe PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In order to reveal the hydration structure of Z-DNA, a neutron diffraction study has been carried out at 1.8 A resolution on a Z-DNA hexamer d(CGCGCG). Neutron diffraction data were collected with the BIX-3 single-crystal diffractometer at the JRR-3 reactor in the Japan Atomic Energy Research Institute (JAERI) using a large crystal (1.6 mm3) obtained from D2O solution. It has been found that almost all the guanine bases have participated in H/D exchange at the C8-H8 group, consistent with the acidic nature of this bond. 44 water molecules were found in the nuclear density maps, of which 29 showed the entire contour of all three atoms (D-O-D). The remaining 15 water molecules had a simple spherical shape, indicating that they were rotationally disordered. An interesting relationship was found between the orientational disorder of the water molecules and their locations. Almost all water molecules in the minor groove were well ordered in the crystal, while 40% of the water molecules in the major groove were rotationally disordered. The hydrogen-bonding networks in the hydration shells have two structural aspects: flexibility and regularity.

-	~~==About this Structure==~~	+	The hydration structure of a Z-DNA hexameric duplex determined by a neutron diffraction technique.,Chatake T, Tanaka I, Umino H, Arai S, Niimura N Acta Crystallogr D Biol Crystallogr. 2005 Aug;61(Pt 8):1088-98. Epub 2005, Jul 20. PMID:16041074<ref>PMID:16041074</ref>
-	~~[[1woe]] is a 2 chain~~ structure. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=1WOE OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Z-DNA\|Z-DNA]]		*[[Z-DNA\|Z-DNA]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:016041074</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
-	[[Category: Arai, S.]]	+	</StructureSection>
-	[[Category: Chatake, T.]]	+	[[Category: Arai, S]]
-	[[Category: Niimura, N.]]	+	[[Category: Chatake, T]]
-	[[Category: Tanaka, I.]]	+	[[Category: Niimura, N]]
-	[[Category: Umino, H.]]	+	[[Category: Tanaka, I]]
		+	[[Category: Umino, H]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Heavy water]]		[[Category: Heavy water]]
	[[Category: Spermine]]		[[Category: Spermine]]
	[[Category: Z-dna]]		[[Category: Z-dna]]

OCA at 05:01, 28 August 2013

OCA — Wed, 28 Aug 2013 05:01:23 GMT

←Older revision		Revision as of 05:01, 28 August 2013
Line 10:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:016041074</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016041074</ref><references group="xtra"/><references/>
	[[Category: Arai, S.]]		[[Category: Arai, S.]]
	[[Category: Chatake, T.]]		[[Category: Chatake, T.]]

OCA at 09:59, 11 March 2013

OCA — Mon, 11 Mar 2013 09:59:16 GMT

←Older revision		Revision as of 09:59, 11 March 2013
Line 1:		Line 1:
-	[[Image:1woe.png\|left\|200px]]
-
	{{STRUCTURE_1woe\| PDB=1woe \| SCENE= }}		{{STRUCTURE_1woe\| PDB=1woe \| SCENE= }}
-
	===X-ray structure of a Z-DNA hexamer d(CGCGCG)===		===X-ray structure of a Z-DNA hexamer d(CGCGCG)===
-
	{{ABSTRACT_PUBMED_16041074}}		{{ABSTRACT_PUBMED_16041074}}

OCA: Protected "1woe" [edit=sysop:move=sysop]

OCA — Tue, 14 Aug 2012 18:37:24 GMT

Protected "1woe" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:37, 14 August 2012