1skp - Revision history

OCA at 09:24, 6 December 2023

OCA — Wed, 06 Dec 2023 09:24:20 GMT

←Older revision		Revision as of 09:24, 6 December 2023
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	==NMR STRUCTURE OF D(GCATATGATAG)(DOT)D(CTATCATATGC): A CONSENSUS SEQUENCE FOR PROMOTERS RECOGNIZED BY SIGMA-K RNA POLYMERASE, 4 STRUCTURES==		==NMR STRUCTURE OF D(GCATATGATAG)(DOT)D(CTATCATATGC): A CONSENSUS SEQUENCE FOR PROMOTERS RECOGNIZED BY SIGMA-K RNA POLYMERASE, 4 STRUCTURES==
-	<StructureSection load='1skp' size='340' side='right'caption='[[1skp~~]], [[NMR_Ensembles_of_Models \| 4 NMR models~~]]' scene=''>	+	<StructureSection load='1skp' size='340' side='right'caption='[[1skp]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1skp]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SKP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1skp]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SKP 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=1skp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1skp OCA], [https://pdbe.org/1skp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1skp RCSB], [https://www.ebi.ac.uk/pdbsum/1skp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1skp ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1skp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1skp OCA], [https://pdbe.org/1skp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1skp RCSB], [https://www.ebi.ac.uk/pdbsum/1skp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1skp ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bianucci~~, A M~~]]	+	[[Category: Bianucci AM]]
-	[[Category: James~~, T L~~]]	+	[[Category: James TL]]
-	[[Category: Lesiak, K]]	+	[[Category: Lesiak K]]
-	[[Category: Ragg, E]]	+	[[Category: Ragg E]]
-	[[Category: Tonelli, M]]	+	[[Category: Tonelli M]]
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Promoter sequence~~]]	+

OCA at 07:33, 22 September 2021

OCA — Wed, 22 Sep 2021 07:33:01 GMT

←Older revision		Revision as of 07:33, 22 September 2021
Line 3:		Line 3:
	<StructureSection load='1skp' size='340' side='right'caption='[[1skp]], [[NMR_Ensembles_of_Models \| 4 NMR models]]' scene=''>		<StructureSection load='1skp' size='340' side='right'caption='[[1skp]], [[NMR_Ensembles_of_Models \| 4 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1skp]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1SKP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1skp]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SKP 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=1skp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1skp OCA], [~~http~~://pdbe.org/1skp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1skp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1skp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1skp 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=1skp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1skp OCA], [https://pdbe.org/1skp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1skp RCSB], [https://www.ebi.ac.uk/pdbsum/1skp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1skp ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:09, 18 December 2019

OCA — Wed, 18 Dec 2019 14:09:09 GMT

←Older revision		Revision as of 14:09, 18 December 2019
Line 1:		Line 1:

	==NMR STRUCTURE OF D(GCATATGATAG)(DOT)D(CTATCATATGC): A CONSENSUS SEQUENCE FOR PROMOTERS RECOGNIZED BY SIGMA-K RNA POLYMERASE, 4 STRUCTURES==		==NMR STRUCTURE OF D(GCATATGATAG)(DOT)D(CTATCATATGC): A CONSENSUS SEQUENCE FOR PROMOTERS RECOGNIZED BY SIGMA-K RNA POLYMERASE, 4 STRUCTURES==
-	<StructureSection load='1skp' size='340' side='right' caption='[[1skp]], [[NMR_Ensembles_of_Models \| 4 NMR models]]' scene=''>	+	<StructureSection load='1skp' size='340' side='right'caption='[[1skp]], [[NMR_Ensembles_of_Models \| 4 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1skp]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SKP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1skp]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SKP FirstGlance]. <br>
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Bianucci, A M]]		[[Category: Bianucci, A M]]
	[[Category: James, T L]]		[[Category: James, T L]]

OCA at 07:50, 14 March 2018

OCA — Wed, 14 Mar 2018 07:50:04 GMT

←Older revision		Revision as of 07:50, 14 March 2018
Line 1:		Line 1:
		+
	==NMR STRUCTURE OF D(GCATATGATAG)(DOT)D(CTATCATATGC): A CONSENSUS SEQUENCE FOR PROMOTERS RECOGNIZED BY SIGMA-K RNA POLYMERASE, 4 STRUCTURES==		==NMR STRUCTURE OF D(GCATATGATAG)(DOT)D(CTATCATATGC): A CONSENSUS SEQUENCE FOR PROMOTERS RECOGNIZED BY SIGMA-K RNA POLYMERASE, 4 STRUCTURES==
	<StructureSection load='1skp' size='340' side='right' caption='[[1skp]], [[NMR_Ensembles_of_Models \| 4 NMR models]]' scene=''>		<StructureSection load='1skp' size='340' side='right' caption='[[1skp]], [[NMR_Ensembles_of_Models \| 4 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1skp]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SKP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1skp]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SKP 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=1skp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1skp OCA], [http://pdbe.org/1skp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1skp RCSB], [http://www.ebi.ac.uk/pdbsum/1skp 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=1skp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1skp OCA], [http://pdbe.org/1skp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1skp RCSB], [http://www.ebi.ac.uk/pdbsum/1skp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1skp ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:32, 10 September 2015

OCA — Thu, 10 Sep 2015 23:32:05 GMT

←Older revision		Revision as of 23:32, 10 September 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1skp]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SKP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1skp]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SKP 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=1skp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1skp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1skp RCSB], [http://www.ebi.ac.uk/pdbsum/1skp 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=1skp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1skp OCA], [http://pdbe.org/1skp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1skp RCSB], [http://www.ebi.ac.uk/pdbsum/1skp PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 13:		Line 13:
	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 1skp" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:30, 22 December 2014

OCA — Mon, 22 Dec 2014 06:30:24 GMT

←Older revision		Revision as of 06:30, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1skp]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SKP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1skp]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SKP FirstGlance]. <br>
-	</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=1skp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1skp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1skp RCSB], [http://www.ebi.ac.uk/pdbsum/1skp 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=1skp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1skp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1skp RCSB], [http://www.ebi.ac.uk/pdbsum/1skp PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bianucci, A M.]]	+	[[Category: Bianucci, A M]]
-	[[Category: James, T L.]]	+	[[Category: James, T L]]
-	[[Category: Lesiak, K.]]	+	[[Category: Lesiak, K]]
-	[[Category: Ragg, E.]]	+	[[Category: Ragg, E]]
-	[[Category: Tonelli, M.]]	+	[[Category: Tonelli, M]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Promoter sequence]]		[[Category: Promoter sequence]]

OCA at 07:03, 9 June 2014

OCA — Mon, 09 Jun 2014 07:03:03 GMT

←Older revision		Revision as of 07:03, 9 June 2014
Line 1:		Line 1:
-	[[~~Image~~:1skp.~~png\|left\|200px~~]]	+	==NMR STRUCTURE OF D(GCATATGATAG)(DOT)D(CTATCATATGC): A CONSENSUS SEQUENCE FOR PROMOTERS RECOGNIZED BY SIGMA-K RNA POLYMERASE, 4 STRUCTURES==
		+	<StructureSection load='1skp' size='340' side='right' caption='[[1skp]], [[NMR_Ensembles_of_Models \| 4 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1skp]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SKP FirstGlance]. <br>
		+	</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=1skp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1skp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1skp RCSB], [http://www.ebi.ac.uk/pdbsum/1skp PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The three-dimensional structure of d(GCATATGATAG).d(CTATCATATGC), from the promoter region of a gene regulating sporulation in Bacillus subtilis mother cells, was determined utilizing two-dimensional nuclear Overhauser effect (2D NOE) and double-quantum-filtered COSY (2QF-COSY) spectra. To minimize the effect of methods used to obtain restraints and refine structure, several variables were studied. Interproton distance bounds were calculated very conservatively by running the complete relaxation matrix program MARDIGRAS hundreds of times using 2D NOE spectra for exchangeable and for nonexchangeable protons at different mixing times, assuming different overall correlation times and different starting structures. The 435 distance restraints were used with two different structural refinement methods: restrained molecular dynamics (rMD) and restrained Monte Carlo calculations (rMC). Refinement using different procedures and starting structures resulted in essentially the same structure (<0.8 A rmsd), indicating that the structure is defined by experimental restraints and not the refinement method or variables used. R factors indicate the structures fit the experimental NOE data very well. Some helical parameters, notably large negative X displacement, are characteristic of A-DNA, but others are characteristic of B-DNA. As with TG.CA steps in other duplex DNA sequences studied in our laboratory, the two TG.CA steps have a positive roll, with T6-G7 exhibiting the largest, and consequently a bent helix axis. The converged structure represents a time-averaged structure. However, multiple conformations, especially in deoxyriboses, were evident from vicinal coupling constants obtained from quantitative simulations of 2QF-COSY cross-peaks and from persistent inconsistencies in experimental distances due to nonlinear conformational averaging.

-	~~{{STRUCTURE_1skp\| PDB=1skp \| SCENE= }}~~	+	Nuclear magnetic resonance structure of d(GCATATGATAG). d(CTATCATATGC): a consensus sequence for promoters recognized by sigma K RNA polymerase.,Tonelli M, Ragg E, Bianucci AM, Lesiak K, James TL Biochemistry. 1998 Aug 25;37(34):11745-61. PMID:9718297<ref>PMID:9718297</ref>

-	~~===NMR STRUCTURE OF D(GCATATGATAG)(DOT)D(CTATCATATGC): A CONSENSUS SEQUENCE FOR PROMOTERS RECOGNIZED BY SIGMA-K RNA POLYMERASE~~, ~~4 STRUCTURES===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9718297}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1skp]] is~~ a ~~2 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1SKP OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:009718297<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Bianucci, A M.]]		[[Category: Bianucci, A M.]]
	[[Category: James, T L.]]		[[Category: James, T L.]]

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

OCA — Tue, 14 Aug 2012 18:38:49 GMT

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

←Older revision

Revision as of 18:38, 14 August 2012

OCA at 18:38, 14 August 2012

OCA — Tue, 14 Aug 2012 18:38:47 GMT

←Older revision		Revision as of 18:38, 14 August 2012
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-	{{Seed}}
	[[Image:1skp.png\|left\|200px]]		[[Image:1skp.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1skp", creates the "Structure Box" on the page.
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-	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_1skp\| PDB=1skp \| SCENE= }}		{{STRUCTURE_1skp\| PDB=1skp \| SCENE= }}

	===NMR STRUCTURE OF D(GCATATGATAG)(DOT)D(CTATCATATGC): A CONSENSUS SEQUENCE FOR PROMOTERS RECOGNIZED BY SIGMA-K RNA POLYMERASE, 4 STRUCTURES===		===NMR STRUCTURE OF D(GCATATGATAG)(DOT)D(CTATCATATGC): A CONSENSUS SEQUENCE FOR PROMOTERS RECOGNIZED BY SIGMA-K RNA POLYMERASE, 4 STRUCTURES===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_9718297}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 9718297 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_9718297}}		{{ABSTRACT_PUBMED_9718297}}

	==About this Structure==		==About this Structure==
-	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKP OCA].	+	[[1skp]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKP OCA].

	==Reference==		==Reference==
-	Nuclear magnetic resonance structure of d(GCATATGATAG). d(CTATCATATGC): a consensus sequence for promoters recognized by sigma K RNA polymerase., Tonelli M, Ragg E, Bianucci AM, Lesiak K, James TL, Biochemistry. 1998 Aug 25;37(34):11745-61. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~9718297 9718297]~~	+	<ref group="xtra">PMID:009718297</ref><references group="xtra"/>
	[[Category: Bianucci, A M.]]		[[Category: Bianucci, A M.]]
	[[Category: James, T L.]]		[[Category: James, T L.]]
Line 29:		Line 17:
	[[Category: Ragg, E.]]		[[Category: Ragg, E.]]
	[[Category: Tonelli, M.]]		[[Category: Tonelli, M.]]
-	[[Category: ~~Nmr structure~~]]	+	[[Category: Dna]]
	[[Category: Promoter sequence]]		[[Category: Promoter sequence]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 14:44:47 2008''

OCA at 11:44, 28 July 2008

OCA — Mon, 28 Jul 2008 11:44:51 GMT

←Older revision		Revision as of 11:44, 28 July 2008
Line 1:		Line 1:
-	[[Image:1skp.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1skp.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_1skp\| PDB=1skp \| SCENE= }}		{{STRUCTURE_1skp\| PDB=1skp \| SCENE= }}

-	~~'''~~NMR STRUCTURE OF D(GCATATGATAG)(DOT)D(CTATCATATGC): A CONSENSUS SEQUENCE FOR PROMOTERS RECOGNIZED BY SIGMA-K RNA POLYMERASE, 4 STRUCTURES~~'''~~	+	===NMR STRUCTURE OF D(GCATATGATAG)(DOT)D(CTATCATATGC): A CONSENSUS SEQUENCE FOR PROMOTERS RECOGNIZED BY SIGMA-K RNA POLYMERASE, 4 STRUCTURES===


-	~~==Overview==~~	+	<!--
-	The ~~three-dimensional structure of d(GCATATGATAG).d(CTATCATATGC)~~, ~~from the promoter region of a gene regulating sporulation in Bacillus subtilis mother cells~~, ~~was determined utilizing two-dimensional nuclear Overhauser effect (2D NOE) and double-quantum-filtered COSY (2QF-COSY) spectra. To minimize~~ the ~~effect of methods used~~ to ~~obtain restraints and refine structure, several variables were studied. Interproton distance bounds were calculated very conservatively by running~~ the ~~complete relaxation matrix program MARDIGRAS hundreds of times using 2D NOE spectra for exchangeable and for nonexchangeable protons~~ at ~~different mixing times, assuming different overall correlation times and different starting structures. The 435 distance restraints were used with two different structural refinement methods~~: ~~restrained molecular dynamics (rMD) and restrained Monte Carlo calculations (rMC)~~. ~~Refinement using different procedures and starting structures resulted in essentially the same structure (<0~~.~~8 A rmsd~~), ~~indicating that the structure~~ is ~~defined by experimental restraints and not~~ the ~~refinement method or variables used~~. ~~R factors indicate the structures fit the experimental NOE data very well. Some helical parameters, notably large negative X displacement, are characteristic of A~~-~~DNA, but others are characteristic of B~~-DNA. As with TG.CA steps in other duplex DNA sequences studied in our laboratory, the two TG.CA steps have a positive roll, with T6-G7 exhibiting the largest, and consequently a bent helix axis. The converged structure represents a time-averaged structure. However, multiple conformations, especially in deoxyriboses, were evident from vicinal coupling constants obtained from quantitative simulations of 2QF-COSY cross-peaks and from persistent inconsistencies in experimental distances due to nonlinear conformational averaging.	+	The line below this paragraph, {{ABSTRACT_PUBMED_9718297}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 9718297 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_9718297}}

	==About this Structure==		==About this Structure==
-	Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKP OCA].	+	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKP OCA].

	==Reference==		==Reference==
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	[[Category: Nmr structure]]		[[Category: Nmr structure]]
	[[Category: Promoter sequence]]		[[Category: Promoter sequence]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 08~~:49:13 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 14:44:47 2008''