5jzq - Revision history

OCA at 19:16, 20 September 2023

OCA — Wed, 20 Sep 2023 19:16:28 GMT

←Older revision		Revision as of 19:16, 20 September 2023
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	<StructureSection load='5jzq' size='340' side='right'caption='[[5jzq]], [[Resolution\|resolution]] 0.78Å' scene=''>		<StructureSection load='5jzq' size='340' side='right'caption='[[5jzq]], [[Resolution\|resolution]] 0.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jzq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JZQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JZQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jzq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JZQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JZQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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]] 0.78Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[1vtu\|1vtu]], [[3p4j\|3p4j]], [[1ick\|1ick]], [[4hif\|4hif]], [[4hig\|4hig]], [[4r15\|4r15]], [[5ebi\|5ebi]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5jzq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jzq OCA], [~~http~~://pdbe.org/5jzq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jzq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jzq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jzq 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=5jzq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jzq OCA], [https://pdbe.org/5jzq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jzq RCSB], [https://www.ebi.ac.uk/pdbsum/5jzq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jzq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Drozdzal, P~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Gilski, M~~]]	+	[[Category: Drozdzal P]]
-	[[Category: ~~Jaskolski,~~ M]]	+	[[Category: Gilski M]]
-	[[Category: ~~Ab initio method]]~~	+	[[Category: Jaskolski M]]
-	~~[[Category: Centrosymmetric space group]]~~	+
-	~~[[Category: Disorder]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Dna enantiomer]]~~	+
-	~~[[Category: Dual-space method]]~~	+
-	~~[[Category: L-ribose nucleic acid]]~~	+
-	~~[[Category: Macromolecular phase problem]]~~	+
-	~~[[Category: Racemate]]~~	+
-	~~[[Category: Self-complementary duplex]]~~	+
-	~~[[Category: Z-dna duplex~~]]	+

OCA at 09:11, 25 June 2020

OCA — Thu, 25 Jun 2020 09:11:57 GMT

←Older revision		Revision as of 09:11, 25 June 2020
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	==Ultrahigh-resolution centrosymmetric crystal structure of Z-DNA reveals massive presence of multiple conformations==		==Ultrahigh-resolution centrosymmetric crystal structure of Z-DNA reveals massive presence of multiple conformations==
-	<StructureSection load='5jzq' size='340' side='right' caption='[[5jzq]], [[Resolution\|resolution]] 0.78Å' scene=''>	+	<StructureSection load='5jzq' size='340' side='right'caption='[[5jzq]], [[Resolution\|resolution]] 0.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jzq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JZQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JZQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jzq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JZQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JZQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vtu\|1vtu]], [[3p4j\|3p4j]], [[1ick\|1ick]], [[4hif\|4hif]], [[4hig\|4hig]], [[4r15\|4r15]], [[5ebi\|5ebi]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vtu\|1vtu]], [[3p4j\|3p4j]], [[1ick\|1ick]], [[4hif\|4hif]], [[4hig\|4hig]], [[4r15\|4r15]], [[5ebi\|5ebi]]</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=5jzq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jzq OCA], [http://pdbe.org/5jzq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jzq RCSB], [http://www.ebi.ac.uk/pdbsum/5jzq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jzq 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=5jzq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jzq OCA], [http://pdbe.org/5jzq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jzq RCSB], [http://www.ebi.ac.uk/pdbsum/5jzq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jzq 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: Drozdzal, P]]		[[Category: Drozdzal, P]]
	[[Category: Gilski, M]]		[[Category: Gilski, M]]

OCA at 14:26, 22 December 2016

OCA — Thu, 22 Dec 2016 14:26:17 GMT

←Older revision		Revision as of 14:26, 22 December 2016
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	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	The ~~crystal structure of a Z~~-~~DNA hexamer duplex~~ d(CGCGCG)(2) ~~determined at ultra high resolution of~~ 0.55 A ~~and refined without restraints~~, ~~displays a high degree of regularity~~ and ~~rigidity in its stereochemistry, in contrast~~ to the ~~more flexible B~~-DNA ~~duplexes~~. The ~~estimations~~ of ~~standard uncertainties of all individually refined parameters, obtained by full~~-~~matrix least~~-~~squares optimization, are comparable with values that are typical for small~~-~~molecule crystallography. The~~ Z-DNA ~~model generated with ultra~~ high~~-resolution diffraction data can be used to revise~~ the ~~stereochemical restraints applied~~ in ~~lower resolution refinements~~. ~~Detailed comparisons~~ of the ~~stereochemical library values with the present accurate Z~~-DNA ~~parameters, shows~~ in ~~general a good agreement, but also reveals significant discrepancies~~ in the ~~description~~ of ~~guanine-sugar valence angles~~ and in the ~~geometry~~ of the ~~phosphate groups~~.	+	The self-complementary d(CGCGCG) hexanucleotide was synthesized with both D-2'-deoxyribose (the natural enantiomer) and L-2'-deoxyribose, and the two enantiomers were mixed in racemic (1:1) proportions and crystallized, producing a new crystal form with C2/c symmetry that diffracted X-rays to 0.78 A resolution. The structure was solved by direct, dual-space and molecular-replacement methods and was refined to an R factor of 13.86%. The asymmetric unit of the crystal contains one Z-DNA duplex and three Mg2+ sites. The crystal structure is comprised of both left-handed (D-form) and right-handed (L-form) Z-DNA duplexes and shows an unexpectedly high degree of structural disorder, which is manifested by the presence of alternate conformations along the DNA backbone chains as well as at four nucleobases (including one base pair) modelled in double conformations. The crystal packing of the presented D/L-DNA-Mg2+ structure exhibits novel DNA hydration patterns and an unusual arrangement of the DNA helices in the unit cell. The paper describes the structure in detail, concentrating on the mode of disorder, and compares the crystal packing of the racemic d(CGCGCG)2 duplex with those of other homochiral and heterochiral Z-DNA structures.

-	~~High regularity~~ of Z-DNA ~~revealed by ultra high-resolution crystal structure at 0~~.~~55 A.,Brzezinski K~~, ~~Brzuszkiewicz A~~, ~~Dauter M, Kubicki~~ M, Jaskolski M~~, Dauter Z Nucleic Acids Res~~. ~~2011 Aug~~ 1;39(14):~~6238~~-48. Epub ~~2011 Apr 1~~. PMID:~~21459852~~<ref>PMID:~~21459852~~</ref>	+	Ultrahigh-resolution centrosymmetric crystal structure of Z-DNA reveals the massive presence of alternate conformations.,Drozdzal P, Gilski M, Jaskolski M Acta Crystallogr D Struct Biol. 2016 Nov 1;72(Pt 11):1203-1211. Epub 2016 Oct 28. PMID:27841753<ref>PMID:27841753</ref>

	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>

OCA at 19:51, 9 December 2016

OCA — Fri, 09 Dec 2016 19:51:51 GMT

←Older revision		Revision as of 19:51, 9 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jzq is ~~ON HOLD until Paper~~ Publication	+	==Ultrahigh-resolution centrosymmetric crystal structure of Z-DNA reveals massive presence of multiple conformations==
		+	<StructureSection load='5jzq' size='340' side='right' caption='[[5jzq]], [[Resolution\|resolution]] 0.78Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5jzq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JZQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JZQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vtu\|1vtu]], [[3p4j\|3p4j]], [[1ick\|1ick]], [[4hif\|4hif]], [[4hig\|4hig]], [[4r15\|4r15]], [[5ebi\|5ebi]]</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=5jzq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jzq OCA], [http://pdbe.org/5jzq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jzq RCSB], [http://www.ebi.ac.uk/pdbsum/5jzq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jzq ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of a Z-DNA hexamer duplex d(CGCGCG)(2) determined at ultra high resolution of 0.55 A and refined without restraints, displays a high degree of regularity and rigidity in its stereochemistry, in contrast to the more flexible B-DNA duplexes. The estimations of standard uncertainties of all individually refined parameters, obtained by full-matrix least-squares optimization, are comparable with values that are typical for small-molecule crystallography. The Z-DNA model generated with ultra high-resolution diffraction data can be used to revise the stereochemical restraints applied in lower resolution refinements. Detailed comparisons of the stereochemical library values with the present accurate Z-DNA parameters, shows in general a good agreement, but also reveals significant discrepancies in the description of guanine-sugar valence angles and in the geometry of the phosphate groups.

-	~~Authors~~:	+	High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A.,Brzezinski K, Brzuszkiewicz A, Dauter M, Kubicki M, Jaskolski M, Dauter Z Nucleic Acids Res. 2011 Aug 1;39(14):6238-48. Epub 2011 Apr 1. PMID:21459852<ref>PMID:21459852</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5jzq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Drozdzal, P]]
		+	[[Category: Gilski, M]]
		+	[[Category: Jaskolski, M]]
		+	[[Category: Ab initio method]]
		+	[[Category: Centrosymmetric space group]]
		+	[[Category: Disorder]]
		+	[[Category: Dna]]
		+	[[Category: Dna enantiomer]]
		+	[[Category: Dual-space method]]
		+	[[Category: L-ribose nucleic acid]]
		+	[[Category: Macromolecular phase problem]]
		+	[[Category: Racemate]]
		+	[[Category: Self-complementary duplex]]
		+	[[Category: Z-dna duplex]]

OCA at 13:17, 20 June 2016

OCA — Mon, 20 Jun 2016 13:17:37 GMT

←Older revision		Revision as of 13:17, 20 June 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5jzq is ON HOLD	+	The entry 5jzq is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5jzq" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:06:43 GMT

Protected "5jzq" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:06, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5jzq is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 01 Jun 2016 14:06:42 GMT

New page: '''Unreleased structure''' The entry 5jzq is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5jzq is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]