409d

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[[Image:409d.gif|left|200px]]
[[Image:409d.gif|left|200px]]
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{{Structure
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|PDB= 409d |SIZE=350|CAPTION= <scene name='initialview01'>409d</scene>, resolution 2.50&Aring;
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The line below this paragraph, containing "STRUCTURE_409d", creates the "Structure Box" on the page.
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|SITE=
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|LIGAND= <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=I:INOSINIC+ACID'>I</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
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|DOMAIN=
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{{STRUCTURE_409d| PDB=409d | SCENE= }}
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|RELATEDENTRY=
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=409d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=409d OCA], [http://www.ebi.ac.uk/pdbsum/409d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=409d RCSB]</span>
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}}
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'''CRYSTAL STRUCTURE OF AN RNA R(CCCIUGGG) WITH THREE INDEPENDENT DUPLEXES INCORPORATING TANDEM I.U WOBBLES'''
'''CRYSTAL STRUCTURE OF AN RNA R(CCCIUGGG) WITH THREE INDEPENDENT DUPLEXES INCORPORATING TANDEM I.U WOBBLES'''
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==About this Structure==
==About this Structure==
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409D 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=409D OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=409D OCA].
==Reference==
==Reference==
Crystal structure of an RNA octamer duplex r(CCCIUGGG)2 incorporating tandem I.U wobbles., Pan B, Mitra SN, Sun L, Hart D, Sundaralingam M, Nucleic Acids Res. 1998 Dec 15;26(24):5699-706. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9838002 9838002]
Crystal structure of an RNA octamer duplex r(CCCIUGGG)2 incorporating tandem I.U wobbles., Pan B, Mitra SN, Sun L, Hart D, Sundaralingam M, Nucleic Acids Res. 1998 Dec 15;26(24):5699-706. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9838002 9838002]
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[[Category: Protein complex]]
 
[[Category: Hart, D.]]
[[Category: Hart, D.]]
[[Category: Mitra, S N.]]
[[Category: Mitra, S N.]]
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[[Category: Sun, L.]]
[[Category: Sun, L.]]
[[Category: Sundaralingam, M.]]
[[Category: Sundaralingam, M.]]
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[[Category: double helix]]
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[[Category: Double helix]]
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[[Category: i u wobble]]
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[[Category: I u wobble]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:16:26 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:36:52 2008''
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Revision as of 19:16, 4 May 2008

Image:409d.gif

Template:STRUCTURE 409d

CRYSTAL STRUCTURE OF AN RNA R(CCCIUGGG) WITH THREE INDEPENDENT DUPLEXES INCORPORATING TANDEM I.U WOBBLES


Overview

The crystal structure of the RNA octamer duplex r(CCCIUGGG)2has been elucidated at 2.5 A resolution. The crystals belong to the space group P21and have unit cell constants a = 33.44 A, b = 43.41 A, c = 49.39 A and beta = 104.7 degrees with three independent duplexes (duplexes 1-3) in the asymmetric unit. The structure was solved by the molecular replacement method and refined to an Rwork/Rfree of 0.185/0.243 using 3765 reflections between 8.0 and 2.5 A. This is the first report of an RNA crystal structure incorporating I.U wobbles and three molecules in the asymmetric unit. Duplex 1 displays a kink of 24 degrees between the mismatch sites, while duplexes 2 and 3 have two kinks each of 19 degrees and 27 degrees, and 24 degrees and 29 degrees, respectively, on either side of the tandem mismatches. At the I.U/U.I mismatch steps, duplex 1 has a twist angle of 33.9 degrees, close to the average for all base pair steps, but duplexes 2 and 3 are underwound, with twist angles of 24.4 degrees and 26.5 degrees, respectively. The tandem I.U wobbles show intrastrand purine-pyrimidine stacking but exhibit interstrand purine-purine stacking with the flanking C.G pairs. The three independent duplexes are stacked non-coaxially in a head-to-tail fashion to form infinite pseudo-continuous helical columns which form intercolumn hydrogen bonding interactions through the 2'-hydroxyl groups where the minor grooves come together.

About this Structure

Full crystallographic information is available from OCA.

Reference

Crystal structure of an RNA octamer duplex r(CCCIUGGG)2 incorporating tandem I.U wobbles., Pan B, Mitra SN, Sun L, Hart D, Sundaralingam M, Nucleic Acids Res. 1998 Dec 15;26(24):5699-706. PMID:9838002 Page seeded by OCA on Sun May 4 22:16:26 2008

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