406d - Revision history

OCA at 10:36, 1 March 2024

2024-03-01T10:36:03Z

←Older revision		Revision as of 10:36, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[406d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=406D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=406D FirstGlance]. <br>		<table><tr><td colspan='2'>[[406d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=406D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=406D FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non~~-~~Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</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]] 1.8Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</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=406d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=406d OCA], [https://pdbe.org/406d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=406d RCSB], [https://www.ebi.ac.uk/pdbsum/406d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=406d 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=406d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=406d OCA], [https://pdbe.org/406d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=406d RCSB], [https://www.ebi.ac.uk/pdbsum/406d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=406d ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The crystal structure of a 17 base RNA oligomer, r(CACCGGAUG GUUCGGUG), has been solved to a resolution of 1.8 A through a combination of molecular replacement, multiple isomorphous replacement phasing, and analysis of observed intensity distributions. The oligomer, which forms a stem-loop in solution, crystallized as a pseudo-infinite duplex in spacegroup P321. The asymmetric unit of the crystal contains four superimposed orientations of the duplex that are out of register, such that backbones superimpose, but base identity differs. This static disorder was initially discovered by brominating a single residue per strand in the sequence, and observing four peaks per strand in difference maps phased with a native molecular replacement solution. The presence of four superimposed duplex "motifs" related by non-crystallographic hypersymmetry was detected by computing <I2>/<I>2 and Wilson ratios for the observed intensities. The observed ratios matched those produced from calculated intensities of a 4-fold statically disordered model. Multi-conformer simulated annealing refinement against a maximum-likelihood target incorporating experimental phase information was used to refine the 4-fold disordered model to an Rfree and R of 29.35% and 25.5%, respectively. The resulting structure reveals four distinct conformations of the duplex, with an average pairwise backbone rmsd of 2.35 A. The structural differences between the four conformations, which can be attributed to differences in packing environment, highlight the possible influence of crystal packing forces on nucleic acid X-ray structures. Analysis of inter-helical packing between symmetry-related molecules reveals an RNA "zipper" that mediates direct phosphate oxygen-2' hydroxyl interactions between close-packed phosphate-sugar backbones. This may be a general mode for RNA tertiary interaction that does not depend on metal ions or primary sequence.
-
-	The 1.8 A crystal structure of a statically disordered 17 base-pair RNA duplex: principles of RNA crystal packing and its effect on nucleic acid structure.,Shah SA, Brunger AT J Mol Biol. 1999 Jan 29;285(4):1577-88. PMID:9917398<ref>PMID:9917398</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 406d" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brunger~~, A T~~]]	+	[[Category: Brunger AT]]
-	[[Category: Shah~~, S A]]~~	+	[[Category: Shah SA]]
-	~~[[Category: Disordered]]~~	+
-	~~[[Category: Double helix]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 07:31, 18 August 2022

2022-08-18T07:31:44Z

←Older revision		Revision as of 07:31, 18 August 2022
Line 1:		Line 1:

	==5'-R(CPAPCPCPGPGPAPUPGPGPUP(BRO) UPCPGPGPUP*G)-3'==		==5'-R(CPAPCPCPGPGPAPUPGPGPUP(BRO) UPCPGPGPUP*G)-3'==
-	<StructureSection load='406d' size='340' side='right' caption='[[406d]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='406d' size='340' side='right'caption='[[406d]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[406d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=406D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=406D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[406d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=406D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=406D FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</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=406d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=406d OCA], [~~http~~://pdbe.org/406d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=406d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/406d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=406d 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=406d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=406d OCA], [https://pdbe.org/406d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=406d RCSB], [https://www.ebi.ac.uk/pdbsum/406d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=406d ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Brunger, A T]]		[[Category: Brunger, A T]]
	[[Category: Shah, S A]]		[[Category: Shah, S A]]

OCA at 11:11, 11 August 2016

2016-08-11T11:11:58Z

←Older revision		Revision as of 11:11, 11 August 2016
Line 1:		Line 1:
		+
	==5'-R(CPAPCPCPGPGPAPUPGPGPUP(BRO) UPCPGPGPUP*G)-3'==		==5'-R(CPAPCPCPGPGPAPUPGPGPUP(BRO) UPCPGPGPUP*G)-3'==
	<StructureSection load='406d' size='340' side='right' caption='[[406d]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='406d' size='340' side='right' caption='[[406d]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[406d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=406D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=406D FirstGlance]. <br>		<table><tr><td colspan='2'>[[406d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=406D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=406D FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</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=406d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=406d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=406d RCSB], [http://www.ebi.ac.uk/pdbsum/406d 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=406d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=406d OCA], [http://pdbe.org/406d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=406d RCSB], [http://www.ebi.ac.uk/pdbsum/406d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=406d ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		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 406d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:49, 4 January 2015

2015-01-04T09:49:50Z

←Older revision		Revision as of 09:49, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[406d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=406D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=406D FirstGlance]. <br>		<table><tr><td colspan='2'>[[406d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=406D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=406D FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</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=406d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=406d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=406d RCSB], [http://www.ebi.ac.uk/pdbsum/406d 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=406d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=406d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=406d RCSB], [http://www.ebi.ac.uk/pdbsum/406d 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 18:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Brunger, A T.]]	+	[[Category: Brunger, A T]]
-	[[Category: Shah, S A.]]	+	[[Category: Shah, S A]]
	[[Category: Disordered]]		[[Category: Disordered]]
	[[Category: Double helix]]		[[Category: Double helix]]
	[[Category: Rna]]		[[Category: Rna]]

OCA at 08:03, 5 June 2014

2014-06-05T08:03:36Z

←Older revision		Revision as of 08:03, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~406d.~~png~~\|~~left\|200px~~]]	+	==5'-R(CPAPCPCPGPGPAPUPGPGPUP(BRO) UPCPGPGPUP*G)-3'==
		+	<StructureSection load='406d' size='340' side='right' caption='[[406d]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[406d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=406D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=406D FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</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=406d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=406d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=406d RCSB], [http://www.ebi.ac.uk/pdbsum/406d PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of a 17 base RNA oligomer, r(CACCGGAUG GUUCGGUG), has been solved to a resolution of 1.8 A through a combination of molecular replacement, multiple isomorphous replacement phasing, and analysis of observed intensity distributions. The oligomer, which forms a stem-loop in solution, crystallized as a pseudo-infinite duplex in spacegroup P321. The asymmetric unit of the crystal contains four superimposed orientations of the duplex that are out of register, such that backbones superimpose, but base identity differs. This static disorder was initially discovered by brominating a single residue per strand in the sequence, and observing four peaks per strand in difference maps phased with a native molecular replacement solution. The presence of four superimposed duplex "motifs" related by non-crystallographic hypersymmetry was detected by computing <I2>/<I>2 and Wilson ratios for the observed intensities. The observed ratios matched those produced from calculated intensities of a 4-fold statically disordered model. Multi-conformer simulated annealing refinement against a maximum-likelihood target incorporating experimental phase information was used to refine the 4-fold disordered model to an Rfree and R of 29.35% and 25.5%, respectively. The resulting structure reveals four distinct conformations of the duplex, with an average pairwise backbone rmsd of 2.35 A. The structural differences between the four conformations, which can be attributed to differences in packing environment, highlight the possible influence of crystal packing forces on nucleic acid X-ray structures. Analysis of inter-helical packing between symmetry-related molecules reveals an RNA "zipper" that mediates direct phosphate oxygen-2' hydroxyl interactions between close-packed phosphate-sugar backbones. This may be a general mode for RNA tertiary interaction that does not depend on metal ions or primary sequence.

-	<!--	+	The 1.8 A crystal structure of a statically disordered 17 base-pair RNA duplex: principles of RNA crystal packing and its effect on nucleic acid structure.,Shah SA, Brunger AT J Mol Biol. 1999 Jan 29;285(4):1577-88. PMID:9917398<ref>PMID:9917398</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_406d"~~, ~~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_406d\| PDB=406d \| SCENE= }}~~	+

-	~~===5'-R(CPAPCPCPGPGPAPUPGPGPUP(BRO) UPCPGPGPUP*G)-3'===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_9917398}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 9917398 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_9917398}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[406d]] is a 2 chain structure. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=406D OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:009917398<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Brunger, A T.]]		[[Category: Brunger, A T.]]
	[[Category: Shah, S A.]]		[[Category: Shah, S A.]]

OCA: Protected "406d" [edit=sysop:move=sysop]

2011-11-16T10:48:29Z

Protected "406d" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:48, 16 November 2011

OCA at 10:48, 16 November 2011

2011-11-16T10:48:27Z

←Older revision		Revision as of 10:48, 16 November 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:406d.png\|left\|200px]]		[[Image:406d.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=406D OCA].	+	[[406d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=406D OCA].

	==Reference==		==Reference==
-	The 1.8 A crystal structure of a statically disordered 17 base-pair RNA duplex: principles of RNA crystal packing and its effect on nucleic acid structure., Shah SA, Brunger AT, J Mol Biol. 1999 Jan 29;285(4):1577-88. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~9917398 9917398]~~	+	<ref group="xtra">PMID:009917398</ref><references group="xtra"/>
	[[Category: Brunger, A T.]]		[[Category: Brunger, A T.]]
	[[Category: Shah, S A.]]		[[Category: Shah, S A.]]
Line 29:		Line 28:
	[[Category: Double helix]]		[[Category: Double helix]]
	[[Category: Rna]]		[[Category: Rna]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 13:15:14 2008''

OCA at 10:15, 3 July 2008

2008-07-03T10:15:14Z

←Older revision		Revision as of 10:15, 3 July 2008
Line 1:		Line 1:
-	[[Image:406d.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:406d.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_406d\| PDB=406d \| SCENE= }}		{{STRUCTURE_406d\| PDB=406d \| SCENE= }}

-	~~'''~~5'-R(CPAPCPCPGPGPAPUPGPGPUP(BRO) UPCPGPGPUP*G)-3'~~'''~~	+	===5'-R(CPAPCPCPGPGPAPUPGPGPUP(BRO) UPCPGPGPUP*G)-3'===


-	~~==Overview==~~	+	<!--
-	The crystal structure of a 17 base RNA oligomer, r(CACCGGAUG GUUCGGUG), has been solved to a resolution of 1.8 A through a combination of molecular replacement, multiple isomorphous replacement phasing, and analysis of observed intensity distributions. The oligomer, which forms a stem-~~loop in solution, crystallized as a pseudo~~-~~infinite duplex in spacegroup P321.~~ The ~~asymmetric unit of the crystal contains four superimposed orientations of the duplex that are out of register~~, ~~such that backbones superimpose~~, ~~but base identity differs. This static disorder was initially discovered by brominating a single residue per strand in~~ the sequence, and observing four peaks per strand in difference maps phased with a native molecular replacement solution. The presence of four superimposed duplex "motifs" related by non-crystallographic hypersymmetry was detected by computing <I2>/<I>2 and Wilson ratios for the observed intensities. The observed ratios matched those produced from calculated intensities of a 4-fold statically disordered model. Multi-conformer simulated annealing refinement against a maximum-likelihood target incorporating experimental phase information was used to ~~refine~~ the ~~4-fold disordered model to an Rfree and R of 29~~.~~35% and 25~~.5%, ~~respectively. The resulting structure reveals four distinct conformations of~~ the ~~duplex, with an average pairwise backbone rmsd of 2~~.35 A. The structural differences between the four conformations, which can be attributed to differences in packing environment, highlight the possible influence of crystal packing forces on nucleic acid X-~~ray structures. Analysis of inter~~-helical packing between symmetry-related molecules reveals an RNA "zipper" that mediates direct phosphate oxygen-2' hydroxyl interactions between close-packed phosphate-sugar backbones. This may be a general mode for RNA tertiary interaction that does not depend on metal ions or primary sequence.	+	The line below this paragraph, {{ABSTRACT_PUBMED_9917398}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 9917398 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_9917398}}

	==About this Structure==		==About this Structure==
Line 25:		Line 29:
	[[Category: Double helix]]		[[Category: Double helix]]
	[[Category: Rna]]		[[Category: Rna]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May~~ ~~4 22~~:16:19 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 13:15:14 2008''

OCA at 19:16, 4 May 2008

2008-05-04T19:16:22Z

←Older revision		Revision as of 19:16, 4 May 2008
Line 1:		Line 1:
	[[Image:406d.gif\|left\|200px]]		[[Image:406d.gif\|left\|200px]]

-	{{Structure	+	<!--
-	\|PDB~~= 406d \|SIZE=350\|CAPTION= <~~scene ~~name='initialview01'>406d</scene>~~, ~~resolution 1~~.~~800Å~~	+	The line below this paragraph, containing "STRUCTURE_406d", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <scene name='pdbligand=5BU:5~~-~~BROMO~~-URIDINE-5'-MONOPHOSPHATE'>5BU</scene>, <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	\|~~ACTIVITY~~=	+	or leave the SCENE parameter empty for the default display.
-	\|~~GENE~~=	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_406d\| PDB=406d \| SCENE= }}
-	~~\|RELATEDENTRY=~~	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=406d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=406d OCA], [http://www.ebi.ac.uk/pdbsum/406d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=406d RCSB]</span>	+
-	}}	+

	'''5'-R(CPAPCPCPGPGPAPUPGPGPUP(BRO) UPCPGPGPUP*G)-3''''		'''5'-R(CPAPCPCPGPGPAPUPGPGPUP(BRO) UPCPGPGPUP*G)-3''''
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	==About this Structure==		==About this Structure==
-	~~406D is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=406D OCA].	+	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=406D OCA].

	==Reference==		==Reference==
	The 1.8 A crystal structure of a statically disordered 17 base-pair RNA duplex: principles of RNA crystal packing and its effect on nucleic acid structure., Shah SA, Brunger AT, J Mol Biol. 1999 Jan 29;285(4):1577-88. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9917398 9917398]		The 1.8 A crystal structure of a statically disordered 17 base-pair RNA duplex: principles of RNA crystal packing and its effect on nucleic acid structure., Shah SA, Brunger AT, J Mol Biol. 1999 Jan 29;285(4):1577-88. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9917398 9917398]
-	[[Category: Protein complex]]
	[[Category: Brunger, A T.]]		[[Category: Brunger, A T.]]
	[[Category: Shah, S A.]]		[[Category: Shah, S A.]]
-	[[Category: ~~disordered~~]]	+	[[Category: Disordered]]
-	[[Category: ~~double~~ helix]]	+	[[Category: Double helix]]
-	[[Category: ~~rna~~]]	+	[[Category: Rna]]
-		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:16:19 2008''
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:36:51 2008''	+

OCA at 02:36, 31 March 2008

2008-03-31T02:36:52Z

←Older revision		Revision as of 02:36, 31 March 2008
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	\|PDB= 406d \|SIZE=350\|CAPTION= <scene name='initialview01'>406d</scene>, resolution 1.800Å		\|PDB= 406d \|SIZE=350\|CAPTION= <scene name='initialview01'>406d</scene>, resolution 1.800Å
	\|SITE=		\|SITE=
-	\|LIGAND=	+	\|LIGAND= <scene name='pdbligand=5BU:5-BROMO-URIDINE-5'-MONOPHOSPHATE'>5BU</scene>, <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>
	\|ACTIVITY=		\|ACTIVITY=
	\|GENE=		\|GENE=
		+	\|DOMAIN=
		+	\|RELATEDENTRY=
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=406d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=406d OCA], [http://www.ebi.ac.uk/pdbsum/406d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=406d RCSB]</span>
	}}		}}

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	[[Category: rna]]		[[Category: rna]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Mar ~~20 19~~:07:55 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:36:51 2008''