1s9b - Revision history

OCA at 08:29, 14 February 2024

OCA — Wed, 14 Feb 2024 08:29:02 GMT

←Older revision		Revision as of 08:29, 14 February 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=1s9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s9b OCA], [https://pdbe.org/1s9b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s9b RCSB], [https://www.ebi.ac.uk/pdbsum/1s9b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s9b 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=1s9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s9b OCA], [https://pdbe.org/1s9b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s9b RCSB], [https://www.ebi.ac.uk/pdbsum/1s9b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s9b ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	DNA oligonucleotides can be used in order to assemble highly structured materials. Oligonucleotides with sticky ends can form long linear structures, whereas branching is required to form two- and three-dimensional nanostructures. In this paper, we show that when Ni(2+) is attached to the N7 atom of guanine, it can also act as a branching point. Thus, we have found that the heptanucleotide d(GAATTCG) can assemble into long linear duplex structures, which cross in space to generate a cubic structure. The three-dimensional arrays are stabilized by phosphate-Ni(2+)-guanine interactions. For the first time, the crystallization of a B form DNA oligonucleotide in a cubic system is reported, space group I23. Large solvent cavities are found among the DNA duplexes.
-
-	A cubic arrangement of DNA double helices based on nickel-guanine interactions.,Valls N, Uson I, Gouyette C, Subirana JA J Am Chem Soc. 2004 Jun 30;126(25):7812-6. PMID:15212528<ref>PMID:15212528</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1s9b" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 21:35, 28 June 2023

OCA — Wed, 28 Jun 2023 21:35:17 GMT

←Older revision		Revision as of 21:35, 28 June 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1s9b]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S9B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S9B FirstGlance]. <br>		<table><tr><td colspan='2'>[[1s9b]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S9B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S9B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 2.81Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=1s9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s9b OCA], [https://pdbe.org/1s9b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s9b RCSB], [https://www.ebi.ac.uk/pdbsum/1s9b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s9b 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=1s9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s9b OCA], [https://pdbe.org/1s9b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s9b RCSB], [https://www.ebi.ac.uk/pdbsum/1s9b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s9b ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gouyette, C]]	+	[[Category: Gouyette C]]
-	[[Category: Subirana~~, J A~~]]	+	[[Category: Subirana JA]]
-	[[Category: Uson, I]]	+	[[Category: Uson I]]
-	[[Category: Valls, N]]	+	[[Category: Valls N]]
-	~~[[Category: Cubic dna]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Double helix]]~~	+
-	~~[[Category: Nickel~~]]	+

OCA at 07:27, 22 September 2021

OCA — Wed, 22 Sep 2021 07:27:50 GMT

←Older revision		Revision as of 07:27, 22 September 2021
Line 3:		Line 3:
	<StructureSection load='1s9b' size='340' side='right'caption='[[1s9b]], [[Resolution\|resolution]] 2.81Å' scene=''>		<StructureSection load='1s9b' size='340' side='right'caption='[[1s9b]], [[Resolution\|resolution]] 2.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1s9b]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S9B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1S9B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1s9b]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S9B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S9B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=1s9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s9b OCA], [~~http~~://pdbe.org/1s9b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1s9b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1s9b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1s9b 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=1s9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s9b OCA], [https://pdbe.org/1s9b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s9b RCSB], [https://www.ebi.ac.uk/pdbsum/1s9b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s9b ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:05, 11 December 2019

OCA — Wed, 11 Dec 2019 19:05:48 GMT

←Older revision		Revision as of 19:05, 11 December 2019
Line 1:		Line 1:

	==Crystal Structure Analysis of the B-DNA GAATTCG==		==Crystal Structure Analysis of the B-DNA GAATTCG==
-	<StructureSection load='1s9b' size='340' side='right' caption='[[1s9b]], [[Resolution\|resolution]] 2.81Å' scene=''>	+	<StructureSection load='1s9b' size='340' side='right'caption='[[1s9b]], [[Resolution\|resolution]] 2.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1s9b]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S9B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S9B FirstGlance]. <br>		<table><tr><td colspan='2'>[[1s9b]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S9B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S9B FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Gouyette, C]]		[[Category: Gouyette, C]]
	[[Category: Subirana, J A]]		[[Category: Subirana, J A]]

OCA at 06:36, 8 March 2018

OCA — Thu, 08 Mar 2018 06:36:54 GMT

←Older revision		Revision as of 06:36, 8 March 2018
Line 1:		Line 1:
		+
	==Crystal Structure Analysis of the B-DNA GAATTCG==		==Crystal Structure Analysis of the B-DNA GAATTCG==
	<StructureSection load='1s9b' size='340' side='right' caption='[[1s9b]], [[Resolution\|resolution]] 2.81Å' scene=''>		<StructureSection load='1s9b' size='340' side='right' caption='[[1s9b]], [[Resolution\|resolution]] 2.81Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1s9b]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S9B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S9B FirstGlance]. <br>		<table><tr><td colspan='2'>[[1s9b]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S9B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S9B FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=1s9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s9b OCA], [http://pdbe.org/1s9b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s9b RCSB], [http://www.ebi.ac.uk/pdbsum/1s9b 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=1s9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s9b OCA], [http://pdbe.org/1s9b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s9b RCSB], [http://www.ebi.ac.uk/pdbsum/1s9b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1s9b ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:59, 11 September 2015

OCA — Fri, 11 Sep 2015 02:59:58 GMT

←Older revision		Revision as of 02:59, 11 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1s9b]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S9B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S9B FirstGlance]. <br>		<table><tr><td colspan='2'>[[1s9b]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S9B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S9B FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=1s9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s9b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s9b RCSB], [http://www.ebi.ac.uk/pdbsum/1s9b 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=1s9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s9b OCA], [http://pdbe.org/1s9b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s9b RCSB], [http://www.ebi.ac.uk/pdbsum/1s9b 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 1s9b" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:07, 15 January 2015

OCA — Thu, 15 Jan 2015 16:07:34 GMT

←Older revision		Revision as of 16:07, 15 January 2015
Line 18:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Gouyette, C.]]	+	[[Category: Gouyette, C]]
-	[[Category: Subirana, J A.]]	+	[[Category: Subirana, J A]]
-	[[Category: Uson, I.]]	+	[[Category: Uson, I]]
-	[[Category: Valls, N.]]	+	[[Category: Valls, N]]
	[[Category: Cubic dna]]		[[Category: Cubic dna]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Double helix]]		[[Category: Double helix]]
	[[Category: Nickel]]		[[Category: Nickel]]

OCA at 08:17, 8 October 2014

OCA — Wed, 08 Oct 2014 08:17:09 GMT

←Older revision		Revision as of 08:17, 8 October 2014
Line 1:		Line 1:
-	[[~~Image:~~1s9b.~~png~~\|~~left\|200px~~]]	+	==Crystal Structure Analysis of the B-DNA GAATTCG==
		+	<StructureSection load='1s9b' size='340' side='right' caption='[[1s9b]], [[Resolution\|resolution]] 2.81Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1s9b]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S9B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S9B FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=1s9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s9b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s9b RCSB], [http://www.ebi.ac.uk/pdbsum/1s9b PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA oligonucleotides can be used in order to assemble highly structured materials. Oligonucleotides with sticky ends can form long linear structures, whereas branching is required to form two- and three-dimensional nanostructures. In this paper, we show that when Ni(2+) is attached to the N7 atom of guanine, it can also act as a branching point. Thus, we have found that the heptanucleotide d(GAATTCG) can assemble into long linear duplex structures, which cross in space to generate a cubic structure. The three-dimensional arrays are stabilized by phosphate-Ni(2+)-guanine interactions. For the first time, the crystallization of a B form DNA oligonucleotide in a cubic system is reported, space group I23. Large solvent cavities are found among the DNA duplexes.

-	~~{{STRUCTURE_1s9b\| PDB=1s9b \| SCENE= }}~~	+	A cubic arrangement of DNA double helices based on nickel-guanine interactions.,Valls N, Uson I, Gouyette C, Subirana JA J Am Chem Soc. 2004 Jun 30;126(25):7812-6. PMID:15212528<ref>PMID:15212528</ref>

-	~~===Crystal Structure Analysis~~ of the ~~B-DNA GAATTCG===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15212528}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[1s9b]] is a 2 chain structure. Full crystallographic information is available from [http:~~//~~oca.weizmann.ac.il/oca-bin/ocashort?id=1S9B OCA].~~	+	</StructureSection>
	[[Category: Gouyette, C.]]		[[Category: Gouyette, C.]]
	[[Category: Subirana, J A.]]		[[Category: Subirana, J A.]]

OCA: Protected "1s9b" [edit=sysop:move=sysop]

OCA — Fri, 04 Jan 2013 10:00:47 GMT

Protected "1s9b" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:00, 4 January 2013

OCA at 10:00, 4 January 2013

OCA — Fri, 04 Jan 2013 10:00:45 GMT

←Older revision		Revision as of 10:00, 4 January 2013
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:1s9b.png\|left\|200px]]
-	[[Image:1s9b.~~gif~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1s9b", 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_1s9b\| PDB=1s9b \| SCENE= }}		{{STRUCTURE_1s9b\| PDB=1s9b \| SCENE= }}

	===Crystal Structure Analysis of the B-DNA GAATTCG===		===Crystal Structure Analysis of the B-DNA GAATTCG===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15212528}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15212528 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_15212528}}		{{ABSTRACT_PUBMED_15212528}}

	==About this Structure==		==About this Structure==
-	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S9B OCA].	+	[[1s9b]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S9B OCA].
-		+
-	~~==Reference==~~	+
-	A cubic arrangement of DNA double helices based on nickel-guanine interactions., Valls N, Uson I, Gouyette C, Subirana JA, J Am Chem Soc. 2004 Jun 30;126(25):7812-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15212528 15212528]	+
	[[Category: Gouyette, C.]]		[[Category: Gouyette, C.]]
	[[Category: Subirana, J A.]]		[[Category: Subirana, J A.]]
Line 29:		Line 14:
	[[Category: Valls, N.]]		[[Category: Valls, N.]]
	[[Category: Cubic dna]]		[[Category: Cubic dna]]
		+	[[Category: Dna]]
	[[Category: Double helix]]		[[Category: Double helix]]
	[[Category: Nickel]]		[[Category: Nickel]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 18:41:44 2008''