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New page: left|200px<br /> <applet load="1sk5" size="450" color="white" frame="true" align="right" spinBox="true" caption="1sk5, resolution 0.89Å" /> '''The ultra-high reso...
 
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[[Image:1sk5.gif|left|200px]]<br />
<applet load="1sk5" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1sk5, resolution 0.89&Aring;" />
'''The ultra-high resolution structure of d(CTTTTAAAAG)2: modulation of bending by T-A steps and its role in DNA recognition'''<br />


==Overview==
==The ultra-high resolution structure of d(CTTTTAAAAG)2: modulation of bending by T-A steps and its role in DNA recognition==
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.
<StructureSection load='1sk5' size='340' side='right'caption='[[1sk5]], [[Resolution|resolution]] 0.89&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1sk5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SK5 FirstGlance]. <br>
1SK5 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1SK5 OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.89&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1sk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sk5 OCA], [https://pdbe.org/1sk5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sk5 RCSB], [https://www.ebi.ac.uk/pdbsum/1sk5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sk5 ProSAT]</span></td></tr>
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11173466 11173466]
</table>
[[Category: Protein complex]]
__TOC__
[[Category: Dickerson, R.E.]]
</StructureSection>
[[Category: Han, G.W.]]
[[Category: Large Structures]]
[[Category: Kopka, M.L.]]
[[Category: Dickerson RE]]
[[Category: Langs, D.]]
[[Category: Han GW]]
[[Category: CA]]
[[Category: Kopka ML]]
[[Category: dna/dna double helix; popypurine tract sequence of hiv-1]]
[[Category: Langs D]]
 
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