321d - Revision history

OCA at 08:39, 7 February 2024

2024-02-07T08:39:01Z

←Older revision		Revision as of 08:39, 7 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[321d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=321D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=321D FirstGlance]. <br>		<table><tr><td colspan='2'>[[321d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=321D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=321D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 2.15Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=321d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=321d OCA], [https://pdbe.org/321d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=321d RCSB], [https://www.ebi.ac.uk/pdbsum/321d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=321d 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=321d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=321d OCA], [https://pdbe.org/321d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=321d RCSB], [https://www.ebi.ac.uk/pdbsum/321d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=321d ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The A-DNA decamer d(CCGGGCCm5CGG) crystallizes in the presence of spermine in three polymorphic forms and with one duplex in the asymmetric unit: hexagonal (P6(1)), unit cell of 55.0 A x 55.0 A x 45.9 A; orthorhombic (P2(1)2(1)2(1)), unit cell of 24.8 A x 44.6 A x 48.0 A, and a second orthorhombic (P2(1)2(1)2(1)), unit cell of 23.6 A x 40.8 A x 43.4 A. The reduction in cell volume among the three different forms is accompanied by a large reduction in solvent content (67% versus 40% versus 24%) and a significant reduction in volume per base-pair (2005 A(3) versus 1325 A(3) versus 1048 A(3)). There is also a concomitant increase in the number of bound spermine molecules per duplex (0 versus 1 versus 2) as well as an increase in DNA bending (10 degrees versus 16 degrees versus 31 degrees), which correspond to major groove widths of 8.0 A versus 4.5 A versus 1.3 A, respectively. The P6(1) crystal form, which represents a new space group for A-DNA decamers, supports one of the most hydrated and extended DNA duplexes to date, while the second orthorhombic form supports one of the least-hydrated and most-condensed non-Z-DNA duplexes. The unmethylated analogue d(CCGGGCCCGG), the double-methyl derivative d(Cm5CGGGCCm5CGG) and the bromine derivative d(CCGGGCC(Br)5CGG) also crystallize in at least two of the aforementioned conformations, and all nine crystal structures were determined. We report, in detail, on the three crystal structures of d(CCGGGCCm5CGG) and the effects of methylation and spermine binding on A-DNA conformation.
-
-	Nine polymorphic crystal structures of d(CCGGGCCCGG), d(CCGGGCCm5CGG), d(Cm5CGGGCCm5CGG) and d(CCGGGCC(Br)5CGG) in three different conformations: effects of spermine binding and methylation on the bending and condensation of A-DNA.,Tippin DB, Sundaralingam M J Mol Biol. 1997 Apr 18;267(5):1171-85. PMID:9150405<ref>PMID:9150405</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 321d" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Sundaralingam, M]]	+	[[Category: Sundaralingam M]]
-	[[Category: Tippin~~, D B]]~~	+	[[Category: Tippin DB]]
-	~~[[Category: A-dna]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Double helix~~]]	+

OCA at 13:23, 4 May 2022

2022-05-04T13:23:37Z

←Older revision		Revision as of 13:23, 4 May 2022
Line 3:		Line 3:
	<StructureSection load='321d' size='340' side='right'caption='[[321d]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='321d' size='340' side='right'caption='[[321d]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[321d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=321D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=321D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[321d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=321D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=321D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=SPM:SPERMINE'>SPM</scene></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=321d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=321d OCA], [~~http~~://pdbe.org/321d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=321d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/321d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=321d 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=321d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=321d OCA], [https://pdbe.org/321d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=321d RCSB], [https://www.ebi.ac.uk/pdbsum/321d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=321d ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 12:13, 29 July 2020

2020-07-29T12:13:11Z

←Older revision		Revision as of 12:13, 29 July 2020
Line 1:		Line 1:

	==CRYSTAL STRUCTURES OF D(CCGGGCCCGG)-ORTHOGONAL FORM==		==CRYSTAL STRUCTURES OF D(CCGGGCCCGG)-ORTHOGONAL FORM==
-	<StructureSection load='321d' size='340' side='right' caption='[[321d]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='321d' size='340' side='right'caption='[[321d]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[321d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=321D OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=321D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[321d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=321D OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=321D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=SPM:SPERMINE'>SPM</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=321d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=321d OCA], [http://pdbe.org/321d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=321d RCSB], [http://www.ebi.ac.uk/pdbsum/321d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=321d 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=321d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=321d OCA], [http://pdbe.org/321d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=321d RCSB], [http://www.ebi.ac.uk/pdbsum/321d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=321d ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Sundaralingam, M]]		[[Category: Sundaralingam, M]]
	[[Category: Tippin, D B]]		[[Category: Tippin, D B]]

OCA at 17:13, 11 August 2016

2016-08-11T17:13:04Z

←Older revision		Revision as of 17:13, 11 August 2016
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURES OF D(CCGGGCCCGG)-ORTHOGONAL FORM==		==CRYSTAL STRUCTURES OF D(CCGGGCCCGG)-ORTHOGONAL FORM==
	<StructureSection load='321d' size='340' side='right' caption='[[321d]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='321d' size='340' side='right' caption='[[321d]], [[Resolution\|resolution]] 2.15Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[321d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=321D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=321D FirstGlance]. <br>		<table><tr><td colspan='2'>[[321d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=321D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=321D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=SPM:SPERMINE'>SPM</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=321d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=321d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=321d RCSB], [http://www.ebi.ac.uk/pdbsum/321d 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=321d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=321d OCA], [http://pdbe.org/321d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=321d RCSB], [http://www.ebi.ac.uk/pdbsum/321d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=321d ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		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 321d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:07, 25 January 2015

2015-01-25T11:07:29Z

←Older revision		Revision as of 11:07, 25 January 2015
Line 18:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Sundaralingam, M.]]	+	[[Category: Sundaralingam, M]]
-	[[Category: Tippin, D B.]]	+	[[Category: Tippin, D B]]
	[[Category: A-dna]]		[[Category: A-dna]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Double helix]]		[[Category: Double helix]]

OCA at 11:49, 29 October 2014

2014-10-29T11:49:43Z

←Older revision		Revision as of 11:49, 29 October 2014
Line 1:		Line 1:
-	[[~~Image:~~321d.~~png~~\|~~left\|200px~~]]	+	==CRYSTAL STRUCTURES OF D(CCGGGCCCGG)-ORTHOGONAL FORM==
		+	<StructureSection load='321d' size='340' side='right' caption='[[321d]], [[Resolution\|resolution]] 2.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[321d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=321D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=321D FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=321d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=321d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=321d RCSB], [http://www.ebi.ac.uk/pdbsum/321d PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The A-DNA decamer d(CCGGGCCm5CGG) crystallizes in the presence of spermine in three polymorphic forms and with one duplex in the asymmetric unit: hexagonal (P6(1)), unit cell of 55.0 A x 55.0 A x 45.9 A; orthorhombic (P2(1)2(1)2(1)), unit cell of 24.8 A x 44.6 A x 48.0 A, and a second orthorhombic (P2(1)2(1)2(1)), unit cell of 23.6 A x 40.8 A x 43.4 A. The reduction in cell volume among the three different forms is accompanied by a large reduction in solvent content (67% versus 40% versus 24%) and a significant reduction in volume per base-pair (2005 A(3) versus 1325 A(3) versus 1048 A(3)). There is also a concomitant increase in the number of bound spermine molecules per duplex (0 versus 1 versus 2) as well as an increase in DNA bending (10 degrees versus 16 degrees versus 31 degrees), which correspond to major groove widths of 8.0 A versus 4.5 A versus 1.3 A, respectively. The P6(1) crystal form, which represents a new space group for A-DNA decamers, supports one of the most hydrated and extended DNA duplexes to date, while the second orthorhombic form supports one of the least-hydrated and most-condensed non-Z-DNA duplexes. The unmethylated analogue d(CCGGGCCCGG), the double-methyl derivative d(Cm5CGGGCCm5CGG) and the bromine derivative d(CCGGGCC(Br)5CGG) also crystallize in at least two of the aforementioned conformations, and all nine crystal structures were determined. We report, in detail, on the three crystal structures of d(CCGGGCCm5CGG) and the effects of methylation and spermine binding on A-DNA conformation.

-	~~{{STRUCTURE_321d\| PDB=321d \| SCENE= }}~~	+	Nine polymorphic crystal structures of d(CCGGGCCCGG), d(CCGGGCCm5CGG), d(Cm5CGGGCCm5CGG) and d(CCGGGCC(Br)5CGG) in three different conformations: effects of spermine binding and methylation on the bending and condensation of A-DNA.,Tippin DB, Sundaralingam M J Mol Biol. 1997 Apr 18;267(5):1171-85. PMID:9150405<ref>PMID:9150405</ref>

-	~~===CRYSTAL STRUCTURES OF D(CCGGGCCCGG)-ORTHOGONAL FORM===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9150405}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[321d]] is~~ a ~~2 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=321D OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:009150405<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Sundaralingam, M.]]		[[Category: Sundaralingam, M.]]
	[[Category: Tippin, D B.]]		[[Category: Tippin, D B.]]

OCA: Protected "321d" [edit=sysop:move=sysop]

2013-01-07T20:12:39Z

Protected "321d" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:12, 7 January 2013

OCA at 20:12, 7 January 2013

2013-01-07T20:12:36Z

←Older revision		Revision as of 20:12, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:321d.png\|left\|200px]]		[[Image:321d.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_321d", 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_321d\| PDB=321d \| SCENE= }}		{{STRUCTURE_321d\| PDB=321d \| SCENE= }}

	===CRYSTAL STRUCTURES OF D(CCGGGCCCGG)-ORTHOGONAL FORM===		===CRYSTAL STRUCTURES OF D(CCGGGCCCGG)-ORTHOGONAL FORM===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_9150405}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 9150405 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_9150405}}		{{ABSTRACT_PUBMED_9150405}}

	==About this Structure==		==About this Structure==
-	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=321D OCA].	+	[[321d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=321D OCA].

	==Reference==		==Reference==
-	Nine polymorphic crystal structures of d(CCGGGCCCGG), d(CCGGGCCm5CGG), d(Cm5CGGGCCm5CGG) and d(CCGGGCC(Br)5CGG) in three different conformations: effects of spermine binding and methylation on the bending and condensation of A-DNA., Tippin DB, Sundaralingam M, J Mol Biol. 1997 Apr 18;267(5):1171-85. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~9150405 9150405]~~	+	<ref group="xtra">PMID:009150405</ref><references group="xtra"/>
	[[Category: Sundaralingam, M.]]		[[Category: Sundaralingam, M.]]
	[[Category: Tippin, D B.]]		[[Category: Tippin, D B.]]
	[[Category: A-dna]]		[[Category: A-dna]]
		+	[[Category: Dna]]
	[[Category: Double helix]]		[[Category: Double helix]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 21:06:27 2008''

OCA at 18:06, 27 July 2008

2008-07-27T18:06:29Z

←Older revision		Revision as of 18:06, 27 July 2008
Line 1:		Line 1:
-	[[Image:321d.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:321d.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_321d\| PDB=321d \| SCENE= }}		{{STRUCTURE_321d\| PDB=321d \| SCENE= }}

-	~~'''~~CRYSTAL STRUCTURES OF D(CCGGGCCCGG)-ORTHOGONAL FORM~~'''~~	+	===CRYSTAL STRUCTURES OF D(CCGGGCCCGG)-ORTHOGONAL FORM===


-	~~==Overview==~~	+	<!--
-	The ~~A-DNA decamer d(CCGGGCCm5CGG) crystallizes in the presence of spermine in three polymorphic forms and with one duplex in the asymmetric unit: hexagonal (P6(1))~~, ~~unit cell of 55.0 A x 55.0 A x 45.9 A; orthorhombic (P2(1)2(1)2(1))~~, ~~unit cell of 24.8 A x 44.6 A x 48.0 A, and a second orthorhombic (P2(1)2(1)2(1)), unit cell of 23.6 A x 40.8 A x 43.4 A. The reduction in cell volume among~~ the three different forms is accompanied by a large reduction in solvent content (67% versus 40% versus 24%) and a significant reduction in volume per base-pair (2005 A(3) versus 1325 A(3) versus 1048 A(3)). There is also a concomitant increase in the ~~number of bound spermine molecules per duplex~~ (~~0 versus 1 versus 2)~~ as ~~well as an increase in DNA bending (10 degrees versus 16 degrees versus 31 degrees), which correspond to major groove widths of 8~~.~~0 A versus 4~~.~~5 A versus 1.3 A, respectively. The P6(1~~) ~~crystal form~~, ~~which represents a new space group for A-DNA decamers, supports one of~~ the ~~most hydrated and extended DNA duplexes to date, while the second orthorhombic form supports one of the least-hydrated and most-condensed non-Z-DNA duplexes~~. ~~The unmethylated analogue d(CCGGGCCCGG), the double~~-methyl derivative d(Cm5CGGGCCm5CGG) and the bromine derivative d(CCGGGCC(Br)5CGG) also crystallize in at least two of the aforementioned conformations, and all nine crystal structures were determined. We report, in detail, on the three crystal structures of d(CCGGGCCm5CGG) and the effects of methylation and spermine binding on A-~~DNA conformation.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_9150405}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 9150405 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_9150405}}

	==About this Structure==		==About this Structure==
Line 24:		Line 28:
	[[Category: A-dna]]		[[Category: A-dna]]
	[[Category: Double helix]]		[[Category: Double helix]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun ~~May 4 20~~:15:41 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 21:06:27 2008''

OCA at 17:15, 4 May 2008

2008-05-04T17:15:42Z

←Older revision		Revision as of 17:15, 4 May 2008
Line 1:		Line 1:
	[[Image:321d.gif\|left\|200px]]		[[Image:321d.gif\|left\|200px]]

-	{{Structure	+	<!--
-	\|PDB~~= 321d \|SIZE=350\|CAPTION= <~~scene ~~name='initialview01'>321d</scene>~~, ~~resolution 2~~.~~150Å~~	+	The line below this paragraph, containing "STRUCTURE_321d", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <scene name='pdbligand=DC:2'~~-~~DEOXYCYTIDINE~~-~~5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene~~>	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	\|~~ACTIVITY~~=	+	or leave the SCENE parameter empty for the default display.
-	\|~~GENE~~=	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_321d\| PDB=321d \| SCENE= }}
-	~~\|RELATEDENTRY=~~	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=321d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=321d OCA], [http://www.ebi.ac.uk/pdbsum/321d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=321d RCSB]</span>	+
-	}}	+

	'''CRYSTAL STRUCTURES OF D(CCGGGCCCGG)-ORTHOGONAL FORM'''		'''CRYSTAL STRUCTURES OF D(CCGGGCCCGG)-ORTHOGONAL FORM'''
Line 19:		Line 16:

	==About this Structure==		==About this Structure==
-	~~321D is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=321D OCA].	+	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=321D OCA].

	==Reference==		==Reference==
	Nine polymorphic crystal structures of d(CCGGGCCCGG), d(CCGGGCCm5CGG), d(Cm5CGGGCCm5CGG) and d(CCGGGCC(Br)5CGG) in three different conformations: effects of spermine binding and methylation on the bending and condensation of A-DNA., Tippin DB, Sundaralingam M, J Mol Biol. 1997 Apr 18;267(5):1171-85. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9150405 9150405]		Nine polymorphic crystal structures of d(CCGGGCCCGG), d(CCGGGCCm5CGG), d(Cm5CGGGCCm5CGG) and d(CCGGGCC(Br)5CGG) in three different conformations: effects of spermine binding and methylation on the bending and condensation of A-DNA., Tippin DB, Sundaralingam M, J Mol Biol. 1997 Apr 18;267(5):1171-85. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9150405 9150405]
-	[[Category: Protein complex]]
	[[Category: Sundaralingam, M.]]		[[Category: Sundaralingam, M.]]
	[[Category: Tippin, D B.]]		[[Category: Tippin, D B.]]
-	[[Category: a-dna]]	+	[[Category: A-dna]]
-	[[Category: ~~double~~ helix]]	+	[[Category: Double helix]]
-		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 20:15:41 2008''
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:21:19 2008''	+