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1sk5
From Proteopedia
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The ultra-high resolution structure of d(CTTTTAAAAG)2: modulation of bending by T-A steps and its role in DNA recognition
Overview
For the first time, ab initio direct methods have been used to solve the, crystal structure of an RNA/DNA hybrid decamer. The RNA/DNA sequence, corresponds to the leftmost two-thirds of the polypurine tract (PPT), the, primer for second-strand DNA synthesis by HIV-1 reverse transcriptase, (RT). Direct methods using Shake-and-Bake (SnB) yielded solutions for the, RNA/DNA decamer molecule using 1.15 A data, which is just on the, resolution edge of what might work with direct methods. Atomic positions, for 96% of the entire molecule, containing 514 non-H atoms including three, Ca(2+) ions, were easily interpreted from a Fourier map based on the, 'Shake-and-Bake' minimal function and CROQUE phase-refinement program., Only six atoms, primarily in the sugar linkage, were missing in this, Fourier map. At present, the R factor of the model is 0.143 (R(free) =, 0.186) for the 562 non-H atom sites located. The conformation of the, RNA/DNA helix is A-form, with a typical A-helix minor-groove width. This, paper presents the methodology used in solving this structure.
About this Structure
1SK5 is a Protein complex structure of sequences from [1] with CA as ligand. Full crystallographic information is available from OCA.
Reference
Direct-methods determination of an RNA/DNA hybrid decamer at 1.15 A resolution., Han GW, Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):213-8. PMID:11173466
Page seeded by OCA on Thu Nov 8 14:29:09 2007
