1ply - Revision history

OCA at 08:09, 14 February 2024

OCA — Wed, 14 Feb 2024 08:09:12 GMT

←Older revision		Revision as of 08:09, 14 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ply]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PLY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PLY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ply]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PLY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PLY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Fiber diffraction, [[Resolution\|Resolution]] 3.2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=1ply FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ply OCA], [https://pdbe.org/1ply PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ply RCSB], [https://www.ebi.ac.uk/pdbsum/1ply PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ply 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=1ply FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ply OCA], [https://pdbe.org/1ply PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ply RCSB], [https://www.ebi.ac.uk/pdbsum/1ply PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ply ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Analysis of X-ray diffraction data from a polycrystalline and well oriented fiber of the sodium salt of poly(dA).poly(dT) shows that this B'-DNA corresponds to a right-handed antiparallel tenfold double-helix of pitch 32.4 A, with C2'-endo furanose rings in both strands. The helix contrasts itself from B-DNA in terms of a very narrow minor groove. Difference electron-density maps have revealed that a continuous spine of water molecules, two per base pair, propagates along this groove with the same symmetry as the DNA and establishes new links between the two strands. In addition to this hydrated DNA helix, the monoclinic unit cell (space group P2(1)) accommodates about 20 sodium ions and 12 water molecules in the vicinity of phosphate groups. These structured guest molecules provide an intricate network of bridges, ranging in size from a single sodium ion to a multiple sodium-water-water-sodium unit, connecting phosphate groups belonging to adjacent DNA helices. The crystallographic R value for this structure is 0.23 for a total of 102 reflections extending out to 3.2 A resolution.
-
-	Sodium ions and water molecules in the structure of poly(dA).poly(dT).,Chandrasekaran R, Radha A, Park HS Acta Crystallogr D Biol Crystallogr. 1995 Nov 1;51(Pt 6):1025-35. PMID:15299771<ref>PMID:15299771</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ply" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:48, 14 June 2023

OCA — Wed, 14 Jun 2023 11:48:38 GMT

←Older revision		Revision as of 11:48, 14 June 2023
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chandrasekaran, R]]	+	[[Category: Chandrasekaran R]]
-	[[Category: Park, H S]]	+	[[Category: Park H-S]]
-	[[Category: Radha, A]]	+	[[Category: Radha A]]
-	~~[[Category: Dna~~]]	+

OCA at 09:31, 8 September 2021

OCA — Wed, 08 Sep 2021 09:31:50 GMT

←Older revision		Revision as of 09:31, 8 September 2021
Line 3:		Line 3:
	<StructureSection load='1ply' size='340' side='right'caption='[[1ply]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='1ply' size='340' side='right'caption='[[1ply]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ply]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PLY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1PLY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ply]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PLY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PLY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=1ply FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ply OCA], [~~http~~://pdbe.org/1ply PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ply RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ply PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ply 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=1ply FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ply OCA], [https://pdbe.org/1ply PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ply RCSB], [https://www.ebi.ac.uk/pdbsum/1ply PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ply ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 1ply" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ply" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA\|DNA]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:29, 27 November 2019

OCA — Wed, 27 Nov 2019 10:29:29 GMT

←Older revision		Revision as of 10:29, 27 November 2019
Line 1:		Line 1:

	==SODIUM IONS AND WATER MOLECULES IN THE STRUCTURE OF POLY D(A)(DOT)POLY D(T)==		==SODIUM IONS AND WATER MOLECULES IN THE STRUCTURE OF POLY D(A)(DOT)POLY D(T)==
-	<StructureSection load='1ply' size='340' side='right' caption='[[1ply]], [[Resolution\|resolution]] 3.20Å' scene=''>	+	<StructureSection load='1ply' size='340' side='right'caption='[[1ply]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ply]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PLY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PLY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ply]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PLY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PLY FirstGlance]. <br>
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Chandrasekaran, R]]		[[Category: Chandrasekaran, R]]
	[[Category: Park, H S]]		[[Category: Park, H S]]
	[[Category: Radha, A]]		[[Category: Radha, A]]
	[[Category: Dna]]		[[Category: Dna]]

OCA at 08:28, 24 February 2018

OCA — Sat, 24 Feb 2018 08:28:59 GMT

←Older revision

Revision as of 08:28, 24 February 2018

OCA at 14:08, 11 September 2015

OCA — Fri, 11 Sep 2015 14:08:05 GMT

←Older revision		Revision as of 14:08, 11 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1ply]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PLY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PLY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ply]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PLY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PLY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=1ply FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ply OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ply RCSB], [http://www.ebi.ac.uk/pdbsum/1ply 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=1ply FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ply OCA], [http://pdbe.org/1ply PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ply RCSB], [http://www.ebi.ac.uk/pdbsum/1ply PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 14:
	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 1ply" style="background-color:#fffaf0;"></div>

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

OCA at 14:10, 17 December 2014

OCA — Wed, 17 Dec 2014 14:10:47 GMT

←Older revision		Revision as of 14:10, 17 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1ply\| PDB=1ply \| SCENE= }}~~	+	==SODIUM IONS AND WATER MOLECULES IN THE STRUCTURE OF POLY D(A)(DOT)POLY D(T)==
-	===SODIUM IONS AND WATER MOLECULES IN THE STRUCTURE OF POLY D(A)(DOT)POLY D(T)===	+	<StructureSection load='1ply' size='340' side='right' caption='[[1ply]], [[Resolution\|resolution]] 3.20Å' scene=''>
-	~~{{ABSTRACT_PUBMED_15299771}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ply]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PLY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PLY FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=1ply FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ply OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ply RCSB], [http://www.ebi.ac.uk/pdbsum/1ply PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Analysis of X-ray diffraction data from a polycrystalline and well oriented fiber of the sodium salt of poly(dA).poly(dT) shows that this B'-DNA corresponds to a right-handed antiparallel tenfold double-helix of pitch 32.4 A, with C2'-endo furanose rings in both strands. The helix contrasts itself from B-DNA in terms of a very narrow minor groove. Difference electron-density maps have revealed that a continuous spine of water molecules, two per base pair, propagates along this groove with the same symmetry as the DNA and establishes new links between the two strands. In addition to this hydrated DNA helix, the monoclinic unit cell (space group P2(1)) accommodates about 20 sodium ions and 12 water molecules in the vicinity of phosphate groups. These structured guest molecules provide an intricate network of bridges, ranging in size from a single sodium ion to a multiple sodium-water-water-sodium unit, connecting phosphate groups belonging to adjacent DNA helices. The crystallographic R value for this structure is 0.23 for a total of 102 reflections extending out to 3.2 A resolution.

-	~~==About this Structure==~~	+	Sodium ions and water molecules in the structure of poly(dA).poly(dT).,Chandrasekaran R, Radha A, Park HS Acta Crystallogr D Biol Crystallogr. 1995 Nov 1;51(Pt 6):1025-35. PMID:15299771<ref>PMID:15299771</ref>
-	~~[[1ply]] is a 2 chain~~ structure. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=1PLY OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[DNA\|DNA]]		*[[DNA\|DNA]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015299771<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
-	[[Category: Chandrasekaran, R.]]	+	</StructureSection>
-	[[Category: Park, H S.]]	+	[[Category: Chandrasekaran, R]]
-	[[Category: Radha, A.]]	+	[[Category: Park, H S]]
		+	[[Category: Radha, A]]
	[[Category: Dna]]		[[Category: Dna]]

OCA at 09:34, 11 March 2013

OCA — Mon, 11 Mar 2013 09:34:41 GMT

←Older revision		Revision as of 09:34, 11 March 2013
Line 1:		Line 1:
-	[[Image:1ply.png\|left\|200px]]
-
	{{STRUCTURE_1ply\| PDB=1ply \| SCENE= }}		{{STRUCTURE_1ply\| PDB=1ply \| SCENE= }}
-
	===SODIUM IONS AND WATER MOLECULES IN THE STRUCTURE OF POLY D(A)(DOT)POLY D(T)===		===SODIUM IONS AND WATER MOLECULES IN THE STRUCTURE OF POLY D(A)(DOT)POLY D(T)===
-
	{{ABSTRACT_PUBMED_15299771}}		{{ABSTRACT_PUBMED_15299771}}

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

OCA — Tue, 14 Aug 2012 16:43:56 GMT

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

←Older revision

Revision as of 16:43, 14 August 2012

OCA at 16:43, 14 August 2012

OCA — Tue, 14 Aug 2012 16:43:55 GMT

←Older revision		Revision as of 16:43, 14 August 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1ply.png\|left\|200px]]		[[Image:1ply.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1ply", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1ply\| PDB=1ply \| SCENE= }}		{{STRUCTURE_1ply\| PDB=1ply \| SCENE= }}

	===SODIUM IONS AND WATER MOLECULES IN THE STRUCTURE OF POLY D(A)(DOT)POLY D(T)===		===SODIUM IONS AND WATER MOLECULES IN THE STRUCTURE OF POLY D(A)(DOT)POLY D(T)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15299771}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15299771 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15299771}}		{{ABSTRACT_PUBMED_15299771}}

	==About this Structure==		==About this Structure==
-	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PLY OCA].	+	[[1ply]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PLY OCA].
		+
		+	==See Also==
		+	*[[DNA\|DNA]]

	==Reference==		==Reference==
-	~~Sodium ions and water molecules in the structure of poly(dA).poly(dT)., Chandrasekaran R, Radha A, Park HS, Acta Crystallogr D Biol Crystallogr. 1995 Nov 1;51(Pt 6):1025-35.~~ PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~15299771 15299771]~~	+	<ref group="xtra">PMID:015299771</ref><references group="xtra"/>
	[[Category: Chandrasekaran, R.]]		[[Category: Chandrasekaran, R.]]
	[[Category: Park, H S.]]		[[Category: Park, H S.]]
	[[Category: Radha, A.]]		[[Category: Radha, A.]]
	[[Category: Dna]]		[[Category: Dna]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 07:35:38 2008''