3qk4 - Revision history

OCA at 08:35, 20 March 2024

OCA — Wed, 20 Mar 2024 08:35:22 GMT

←Older revision		Revision as of 08:35, 20 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3qk4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QK4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3qk4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QK4 FirstGlance]. <br>
-	</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=3qk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qk4 OCA], [https://pdbe.org/3qk4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qk4 RCSB], [https://www.ebi.ac.uk/pdbsum/3qk4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qk4 ProSAT]</span></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]] 2.6Å</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=3qk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qk4 OCA], [https://pdbe.org/3qk4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qk4 RCSB], [https://www.ebi.ac.uk/pdbsum/3qk4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qk4 ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	We report the 2.6A resolution crystal structure of the tetra-decamer d(CGCGGGTACCCGCG) in the tetragonal space group P4(3). This sequence contains the KpnI restriction site GGTACC in the centre which is flanked by alternating 'CG' sequences, and has a 'TA' step at the centre. These are features could favour the left-handed Z type helix. Despite this, overall the molecule has the A form. This is the first tetra-decamer crystallized in the A-DNA conformation, i.e. more than one full turn of the A helix. The crystallographic asymmetric unit consists of one tetra-decamer duplex. The helical twist and slide, as well as the base pair-base pair stacking interactions show alternations at the alternating pyrimidine-purine and purine-pyrimidine base steps. This variation is reminiscent of the dinucleotide repeat in left-handed Z-DNA helices. The crystal packing is unlike other A-DNA crystal structures, with each helix having a large number of contacts of many different types with symmetry-related neighbours.
-
-	The structure of a full turn of an A-DNA duplex d(CGCGGGTACCCGCG)(2).,Venkadesh S, Mandal PK, Gautham N Biochem Biophys Res Commun. 2011 Apr 8;407(2):307-12. Epub 2011 Mar 21. PMID:21397589<ref>PMID:21397589</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3qk4" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gautham, N]]	+	[[Category: Gautham N]]
-	[[Category: Mandal~~, P K~~]]	+	[[Category: Mandal PK]]
-	[[Category: Venkadesh, S]]	+	[[Category: Venkadesh S]]
-	~~[[Category: A-dna duplex]]~~	+
-	~~[[Category: Dna~~]]	+

OCA at 06:12, 8 June 2022

OCA — Wed, 08 Jun 2022 06:12:10 GMT

←Older revision		Revision as of 06:12, 8 June 2022
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	==Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex==		==Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex==
-	<StructureSection load='3qk4' size='340' side='right' caption='[[3qk4]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='3qk4' size='340' side='right'caption='[[3qk4]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qk4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QK4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3QK4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qk4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QK4 FirstGlance]. <br>
-	</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=3qk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qk4 OCA], [~~http~~://pdbe.org/3qk4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3qk4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3qk4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3qk4 ProSAT]</span></td></tr>	+	</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=3qk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qk4 OCA], [https://pdbe.org/3qk4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qk4 RCSB], [https://www.ebi.ac.uk/pdbsum/3qk4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qk4 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Gautham, N]]		[[Category: Gautham, N]]
	[[Category: Mandal, P K]]		[[Category: Mandal, P K]]

OCA at 09:03, 5 August 2016

OCA — Fri, 05 Aug 2016 09:03:54 GMT

←Older revision		Revision as of 09:03, 5 August 2016
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		+
	==Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex==		==Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex==
	<StructureSection load='3qk4' size='340' side='right' caption='[[3qk4]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3qk4' size='340' side='right' caption='[[3qk4]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3qk4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QK4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QK4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3qk4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QK4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QK4 FirstGlance]. <br>
-	</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=3qk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qk4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qk4 RCSB], [http://www.ebi.ac.uk/pdbsum/3qk4 PDBsum]</span></td></tr>	+	</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=3qk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qk4 OCA], [http://pdbe.org/3qk4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qk4 RCSB], [http://www.ebi.ac.uk/pdbsum/3qk4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qk4 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 3qk4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:04, 19 December 2014

OCA — Fri, 19 Dec 2014 11:04:39 GMT

←Older revision		Revision as of 11:04, 19 December 2014
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-	~~{{STRUCTURE_3qk4\| PDB=3qk4 \| SCENE= }}~~	+	==Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex==
-	===Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex===	+	<StructureSection load='3qk4' size='340' side='right' caption='[[3qk4]], [[Resolution\|resolution]] 2.60Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21397589}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3qk4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QK4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QK4 FirstGlance]. <br>
		+	</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=3qk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qk4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qk4 RCSB], [http://www.ebi.ac.uk/pdbsum/3qk4 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We report the 2.6A resolution crystal structure of the tetra-decamer d(CGCGGGTACCCGCG) in the tetragonal space group P4(3). This sequence contains the KpnI restriction site GGTACC in the centre which is flanked by alternating 'CG' sequences, and has a 'TA' step at the centre. These are features could favour the left-handed Z type helix. Despite this, overall the molecule has the A form. This is the first tetra-decamer crystallized in the A-DNA conformation, i.e. more than one full turn of the A helix. The crystallographic asymmetric unit consists of one tetra-decamer duplex. The helical twist and slide, as well as the base pair-base pair stacking interactions show alternations at the alternating pyrimidine-purine and purine-pyrimidine base steps. This variation is reminiscent of the dinucleotide repeat in left-handed Z-DNA helices. The crystal packing is unlike other A-DNA crystal structures, with each helix having a large number of contacts of many different types with symmetry-related neighbours.

-	~~==About this Structure==~~	+	The structure of a full turn of an A-DNA duplex d(CGCGGGTACCCGCG)(2).,Venkadesh S, Mandal PK, Gautham N Biochem Biophys Res Commun. 2011 Apr 8;407(2):307-12. Epub 2011 Mar 21. PMID:21397589<ref>PMID:21397589</ref>
-	~~[[3qk4]] is~~ a 2 ~~chain structure~~. ~~Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3QK4 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:021397589</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Gautham, N.]]	+	== References ==
-	[[Category: Mandal, P K.]]	+	<references/>
-	[[Category: Venkadesh, S.]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Gautham, N]]
		+	[[Category: Mandal, P K]]
		+	[[Category: Venkadesh, S]]
	[[Category: A-dna duplex]]		[[Category: A-dna duplex]]
	[[Category: Dna]]		[[Category: Dna]]

OCA at 08:28, 8 May 2013

OCA — Wed, 08 May 2013 08:28:53 GMT

←Older revision		Revision as of 08:28, 8 May 2013
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-	[[Image:3qk4.png\|left\|200px]]
-
-	<!--
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-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
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-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3qk4\| PDB=3qk4 \| SCENE= }}		{{STRUCTURE_3qk4\| PDB=3qk4 \| SCENE= }}
-
	===Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex===		===Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21397589}}, adds the Publication Abstract to the page
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	{{ABSTRACT_PUBMED_21397589}}		{{ABSTRACT_PUBMED_21397589}}

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	==Reference==		==Reference==
-	<ref group="xtra">PMID:021397589</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021397589</ref><references group="xtra"/><references/>
	[[Category: Gautham, N.]]		[[Category: Gautham, N.]]
	[[Category: Mandal, P K.]]		[[Category: Mandal, P K.]]
	[[Category: Venkadesh, S.]]		[[Category: Venkadesh, S.]]
		+	[[Category: A-dna duplex]]
		+	[[Category: Dna]]

OCA at 05:40, 18 May 2011

OCA — Wed, 18 May 2011 05:40:51 GMT

←Older revision		Revision as of 05:40, 18 May 2011
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-	[[Image:3qk4.~~jpg~~\|left\|200px]]	+	[[Image:3qk4.png\|left\|200px]]

	<!--		<!--
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	===Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex===		===Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21397589}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21397589 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21397589}}

	==About this Structure==		==About this Structure==
	[[3qk4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QK4 OCA].		[[3qk4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QK4 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021397589</ref><references group="xtra"/>
	[[Category: Gautham, N.]]		[[Category: Gautham, N.]]
	[[Category: Mandal, P K.]]		[[Category: Mandal, P K.]]
	[[Category: Venkadesh, S.]]		[[Category: Venkadesh, S.]]

OCA at 07:09, 2 March 2011

OCA — Wed, 02 Mar 2011 07:09:10 GMT

←Older revision		Revision as of 07:09, 2 March 2011
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-	~~'''Unreleased structure'''~~	+	[[Image:3qk4.jpg\|left\|200px]]

-	The ~~entry 3qk4~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3qk4", 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_3qk4\| PDB=3qk4 \| SCENE= }}

-	~~Authors: Venkadesh, S., Mandal, P.K., Gautham, N.~~	+	===Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex===

-	~~Description: Crystal structure of d(CGCGGGTACCCGCG)~~2 ~~as A~~-~~DNA duplex~~	+
		+	==About this Structure==
		+	[[3qk4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QK4 OCA].
		+	[[Category: Gautham, N.]]
		+	[[Category: Mandal, P K.]]
		+	[[Category: Venkadesh, S.]]

OCA at 09:38, 23 February 2011

OCA — Wed, 23 Feb 2011 09:38:17 GMT

←Older revision		Revision as of 09:38, 23 February 2011
Line 3:		Line 3:
	The entry 3qk4 is ON HOLD		The entry 3qk4 is ON HOLD

-	Authors: Venkadesh, S., Mandal, P.K.	+	Authors: Venkadesh, S., Mandal, P.K., Gautham, N.

	Description: Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex		Description: Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex

OCA: Protected "3qk4" [edit=sysop:move=sysop]

OCA — Wed, 09 Feb 2011 05:50:52 GMT

Protected "3qk4" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:50, 9 February 2011

OCA: New page: '''Unreleased structure''' The entry 3qk4 is ON HOLD Authors: Venkadesh, S., Mandal, P.K. Description: Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex

OCA — Wed, 09 Feb 2011 05:50:52 GMT

New page: '''Unreleased structure''' The entry 3qk4 is ON HOLD Authors: Venkadesh, S., Mandal, P.K. Description: Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex

New page

'''Unreleased structure'''

The entry 3qk4 is ON HOLD

Authors: Venkadesh, S., Mandal, P.K.

Description: Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex