1da3 - Revision history

OCA at 06:51, 7 February 2024

OCA — Wed, 07 Feb 2024 06:51:15 GMT

←Older revision		Revision as of 06:51, 7 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1da3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DA3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1da3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DA3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1da3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1da3 OCA], [https://pdbe.org/1da3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1da3 RCSB], [https://www.ebi.ac.uk/pdbsum/1da3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1da3 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=1da3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1da3 OCA], [https://pdbe.org/1da3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1da3 RCSB], [https://www.ebi.ac.uk/pdbsum/1da3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1da3 ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The B-DNA decanucleotide C-G-A-T-C-G-6meA-T-C-G has been crystallized under the same conditions used earlier for C-G-A-T-C-G-A-T-C-G, but is found to adopt a new trigonal P3(2)21 packing mode instead of the expected orthorhombic P2(1)2(1)2(1) form. Unit cell dimensions a = b = 33.38 A, c = 98.30 A, gamma = 120 degrees, imply ten base-pairs or one complete decamer double helix per asymmetric unit. The 2282 two-sigma data to 2.0 A refine to R = 17.2% with 45 water molecules, 1.5 hexavalent hydrated magnesium complexes, and 0.5 chloride ion per asymmetric unit. Neighboring helices interlock backbone chains and major grooves, crossing at an angle of 120 degrees in a manner that yields an excellent model for a Holliday junction. Local helix parameters differ markedly in the trigonal and orthorhombic structures, with the trigonal helix exhibiting behavior closer to that expected of B-DNA in solution. The trigonal form has an average of 10.6 base-pairs per turn, in contrast to 9.7 base-pairs per turn in the orthorhombic cell. A comparison of all known B-DNA decamer and dodecamer crystal structure analyses indicates that, the greater the cell volume per base-pair (and hence the more open the crystal structure), the closer the mean helix twist approaches an expected 10.6 base-pairs per turn.
-
-	The crystal structure of the trigonal decamer C-G-A-T-C-G-6meA-T-C-G: a B-DNA helix with 10.6 base-pairs per turn.,Baikalov I, Grzeskowiak K, Yanagi K, Quintana J, Dickerson RE J Mol Biol. 1993 Jun 5;231(3):768-84. PMID:8515450<ref>PMID:8515450</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1da3" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:35, 14 December 2022

OCA — Wed, 14 Dec 2022 10:35:56 GMT

←Older revision		Revision as of 10:35, 14 December 2022
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1da3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DA3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1da3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DA3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:~~CHLORIDE+ION~~'>CL</scene>, <scene name='pdbligand=MG:~~MAGNESIUM~~+ION'>MG</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~6MA~~:~~N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE~~'>~~6MA~~</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=1da3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1da3 OCA], [https://pdbe.org/1da3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1da3 RCSB], [https://www.ebi.ac.uk/pdbsum/1da3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1da3 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=1da3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1da3 OCA], [https://pdbe.org/1da3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1da3 RCSB], [https://www.ebi.ac.uk/pdbsum/1da3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1da3 ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Baikalov, I]]	+	[[Category: Baikalov I]]
-	[[Category: Dickerson~~, R E~~]]	+	[[Category: Dickerson RE]]
-	[[Category: Grzeskowiak, K]]	+	[[Category: Grzeskowiak K]]
-	[[Category: Quintana, J]]	+	[[Category: Quintana J]]
-	[[Category: Yanagi, K]]	+	[[Category: Yanagi K]]
-	~~[[Category: B-dna]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Double helix]]~~	+
-	~~[[Category: Modified~~]]	+

OCA at 18:23, 10 March 2021

OCA — Wed, 10 Mar 2021 18:23:28 GMT

←Older revision		Revision as of 18:23, 10 March 2021
Line 3:		Line 3:
	<StructureSection load='1da3' size='340' side='right'caption='[[1da3]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1da3' size='340' side='right'caption='[[1da3]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1da3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DA3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1DA3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1da3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DA3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</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=1da3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1da3 OCA], [~~http~~://pdbe.org/1da3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1da3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1da3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1da3 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=1da3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1da3 OCA], [https://pdbe.org/1da3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1da3 RCSB], [https://www.ebi.ac.uk/pdbsum/1da3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1da3 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:08, 6 June 2019

OCA — Thu, 06 Jun 2019 00:08:43 GMT

←Older revision		Revision as of 00:08, 6 June 2019
Line 1:		Line 1:

	==THE CRYSTAL STRUCTURE OF THE TRIGONAL DECAMER C-G-A-T-C-G-6MEA-T-C-G: A B-DNA HELIX WITH 10.6 BASE-PAIRS PER TURN==		==THE CRYSTAL STRUCTURE OF THE TRIGONAL DECAMER C-G-A-T-C-G-6MEA-T-C-G: A B-DNA HELIX WITH 10.6 BASE-PAIRS PER TURN==
-	<StructureSection load='1da3' size='340' side='right' caption='[[1da3]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1da3' size='340' side='right'caption='[[1da3]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1da3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DA3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DA3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1da3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DA3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DA3 FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Baikalov, I]]		[[Category: Baikalov, I]]
	[[Category: Dickerson, R E]]		[[Category: Dickerson, R E]]

OCA at 04:08, 30 August 2017

OCA — Wed, 30 Aug 2017 04:08:52 GMT

←Older revision		Revision as of 04:08, 30 August 2017
Line 1:		Line 1:
		+
	==THE CRYSTAL STRUCTURE OF THE TRIGONAL DECAMER C-G-A-T-C-G-6MEA-T-C-G: A B-DNA HELIX WITH 10.6 BASE-PAIRS PER TURN==		==THE CRYSTAL STRUCTURE OF THE TRIGONAL DECAMER C-G-A-T-C-G-6MEA-T-C-G: A B-DNA HELIX WITH 10.6 BASE-PAIRS PER TURN==
	<StructureSection load='1da3' size='340' side='right' caption='[[1da3]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1da3' size='340' side='right' caption='[[1da3]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</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=1da3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1da3 OCA], [http://pdbe.org/1da3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1da3 RCSB], [http://www.ebi.ac.uk/pdbsum/1da3 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=1da3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1da3 OCA], [http://pdbe.org/1da3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1da3 RCSB], [http://www.ebi.ac.uk/pdbsum/1da3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1da3 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:59, 10 September 2015

OCA — Thu, 10 Sep 2015 01:59:31 GMT

←Older revision		Revision as of 01:59, 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</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=1da3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1da3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1da3 RCSB], [http://www.ebi.ac.uk/pdbsum/1da3 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=1da3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1da3 OCA], [http://pdbe.org/1da3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1da3 RCSB], [http://www.ebi.ac.uk/pdbsum/1da3 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 1da3" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:07, 22 December 2014

OCA — Mon, 22 Dec 2014 23:07:32 GMT

←Older revision		Revision as of 23:07, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1da3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DA3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DA3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1da3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DA3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DA3 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1da3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1da3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1da3 RCSB], [http://www.ebi.ac.uk/pdbsum/1da3 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=1da3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1da3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1da3 RCSB], [http://www.ebi.ac.uk/pdbsum/1da3 PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baikalov, I.]]	+	[[Category: Baikalov, I]]
-	[[Category: Dickerson, R E.]]	+	[[Category: Dickerson, R E]]
-	[[Category: Grzeskowiak, K.]]	+	[[Category: Grzeskowiak, K]]
-	[[Category: Quintana, J.]]	+	[[Category: Quintana, J]]
-	[[Category: Yanagi, K.]]	+	[[Category: Yanagi, K]]
	[[Category: B-dna]]		[[Category: B-dna]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Double helix]]		[[Category: Double helix]]
	[[Category: Modified]]		[[Category: Modified]]

OCA at 06:38, 4 September 2014

OCA — Thu, 04 Sep 2014 06:38:09 GMT

←Older revision		Revision as of 06:38, 4 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1da3.~~png~~\|~~left~~\|~~200px~~]]	+	==THE CRYSTAL STRUCTURE OF THE TRIGONAL DECAMER C-G-A-T-C-G-6MEA-T-C-G: A B-DNA HELIX WITH 10.6 BASE-PAIRS PER TURN==
		+	<StructureSection load='1da3' size='340' side='right' caption='[[1da3]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1da3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DA3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DA3 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1da3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1da3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1da3 RCSB], [http://www.ebi.ac.uk/pdbsum/1da3 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The B-DNA decanucleotide C-G-A-T-C-G-6meA-T-C-G has been crystallized under the same conditions used earlier for C-G-A-T-C-G-A-T-C-G, but is found to adopt a new trigonal P3(2)21 packing mode instead of the expected orthorhombic P2(1)2(1)2(1) form. Unit cell dimensions a = b = 33.38 A, c = 98.30 A, gamma = 120 degrees, imply ten base-pairs or one complete decamer double helix per asymmetric unit. The 2282 two-sigma data to 2.0 A refine to R = 17.2% with 45 water molecules, 1.5 hexavalent hydrated magnesium complexes, and 0.5 chloride ion per asymmetric unit. Neighboring helices interlock backbone chains and major grooves, crossing at an angle of 120 degrees in a manner that yields an excellent model for a Holliday junction. Local helix parameters differ markedly in the trigonal and orthorhombic structures, with the trigonal helix exhibiting behavior closer to that expected of B-DNA in solution. The trigonal form has an average of 10.6 base-pairs per turn, in contrast to 9.7 base-pairs per turn in the orthorhombic cell. A comparison of all known B-DNA decamer and dodecamer crystal structure analyses indicates that, the greater the cell volume per base-pair (and hence the more open the crystal structure), the closer the mean helix twist approaches an expected 10.6 base-pairs per turn.

-	~~{{STRUCTURE_1da3\| PDB=1da3 \| SCENE= }}~~	+	The crystal structure of the trigonal decamer C-G-A-T-C-G-6meA-T-C-G: a B-DNA helix with 10.6 base-pairs per turn.,Baikalov I, Grzeskowiak K, Yanagi K, Quintana J, Dickerson RE J Mol Biol. 1993 Jun 5;231(3):768-84. PMID:8515450<ref>PMID:8515450</ref>

-	~~===THE CRYSTAL STRUCTURE OF THE TRIGONAL DECAMER C-G-A-T-C-G-6MEA-T-C-G: A B-DNA HELIX WITH 10.6 BASE-PAIRS PER TURN===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_8515450}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1da3]] is~~ a ~~2 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1DA3 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:008515450<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Baikalov, I.]]		[[Category: Baikalov, I.]]
	[[Category: Dickerson, R E.]]		[[Category: Dickerson, R E.]]

OCA: Protected "1da3" [edit=sysop:move=sysop]

OCA — Sun, 21 Oct 2012 20:39:20 GMT

Protected "1da3" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:39, 21 October 2012

OCA at 20:39, 21 October 2012

OCA — Sun, 21 Oct 2012 20:39:17 GMT

←Older revision		Revision as of 20:39, 21 October 2012
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-	{{Seed}}
	[[Image:1da3.png\|left\|200px]]		[[Image:1da3.png\|left\|200px]]

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	{{STRUCTURE_1da3\| PDB=1da3 \| SCENE= }}		{{STRUCTURE_1da3\| PDB=1da3 \| SCENE= }}

	===THE CRYSTAL STRUCTURE OF THE TRIGONAL DECAMER C-G-A-T-C-G-6MEA-T-C-G: A B-DNA HELIX WITH 10.6 BASE-PAIRS PER TURN===		===THE CRYSTAL STRUCTURE OF THE TRIGONAL DECAMER C-G-A-T-C-G-6MEA-T-C-G: A B-DNA HELIX WITH 10.6 BASE-PAIRS PER TURN===

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	{{ABSTRACT_PUBMED_8515450}}		{{ABSTRACT_PUBMED_8515450}}

	==About this Structure==		==About this Structure==
-	~~1DA3~~ is a 2 ~~chains~~ structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DA3 OCA].	+	[[1da3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DA3 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~8515450~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:008515450</ref><references group="xtra"/>
	[[Category: Baikalov, I.]]		[[Category: Baikalov, I.]]
	[[Category: Dickerson, R E.]]		[[Category: Dickerson, R E.]]
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	[[Category: Yanagi, K.]]		[[Category: Yanagi, K.]]
	[[Category: B-dna]]		[[Category: B-dna]]
		+	[[Category: Dna]]
	[[Category: Double helix]]		[[Category: Double helix]]
	[[Category: Modified]]		[[Category: Modified]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 27 14:43:47 2009''