1sk5

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[[Image:1sk5.gif|left|200px]]
 
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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==
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The line below this paragraph, containing "STRUCTURE_1sk5", creates the "Structure Box" on the page.
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<StructureSection load='1sk5' size='340' side='right'caption='[[1sk5]], [[Resolution|resolution]] 0.89&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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</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>
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<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>
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{{STRUCTURE_1sk5| PDB=1sk5 | SCENE= }}
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<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>
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</table>
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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'''
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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==Overview==
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[[Category: Dickerson RE]]
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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.
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[[Category: Han GW]]
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[[Category: Kopka ML]]
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==About this Structure==
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[[Category: Langs D]]
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SK5 OCA].
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==Reference==
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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://www.ncbi.nlm.nih.gov/pubmed/11173466 11173466]
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[[Category: Dickerson, R E.]]
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[[Category: Han, G W.]]
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[[Category: Kopka, M L.]]
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[[Category: Langs, D.]]
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[[Category: Dna/dna double helix]]
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[[Category: Popypurine tract sequence of hiv-1]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 08:48:20 2008''
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Current revision

The ultra-high resolution structure of d(CTTTTAAAAG)2: modulation of bending by T-A steps and its role in DNA recognition

PDB ID 1sk5

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