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1vj4

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[[Image:1vj4.gif|left|200px]]
 
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{{Structure
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==SEQUENCE-DEPENDENT CONFORMATION OF AN A-DNA DOUBLE HELIX: THE CRYSTAL STRUCTURE OF THE OCTAMER D(G-G-T-A-T-A-C-C)==
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|PDB= 1vj4 |SIZE=350|CAPTION= <scene name='initialview01'>1vj4</scene>, resolution 1.800&Aring;
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<StructureSection load='1vj4' size='340' side='right'caption='[[1vj4]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND=
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<table><tr><td colspan='2'>[[1vj4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VJ4 FirstGlance]. <br>
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|ACTIVITY=
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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]] 1.8&#8491;</td></tr>
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|GENE=
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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=1vj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vj4 OCA], [https://pdbe.org/1vj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vj4 RCSB], [https://www.ebi.ac.uk/pdbsum/1vj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vj4 ProSAT]</span></td></tr>
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}}
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</table>
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__TOC__
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'''SEQUENCE-DEPENDENT CONFORMATION OF AN A-DNA DOUBLE HELIX: THE CRYSTAL STRUCTURE OF THE OCTAMER D(G-G-T-A-T-A-C-C)'''
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Cruse WB]]
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==Overview==
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[[Category: Kennard O]]
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The crystal structures of the synthetic self-complementary octamer d(G-G-T-A-T-A-C-C) and its 5-bromouracil-containing analogue have been refined to R values of 20% and 14% at resolutions of 1.8 and 2.25 A, respectively. The molecules adopt and A-DNA type double-helical conformation, which is minimally affected by crystal forces. A detailed analysis of the structure shows a considerable influence of the nucleotide sequence on the base-pair stacking patterns. In particular, the electrostatic stacking interactions between adjacent guanine and thymine bases produce symmetric bending of the double helix and a major-groove widening. The sugar-phosphate backbone appears to be only slightly affected by the base sequence. The local variations in the base-pair orientation are brought about by correlated adjustments in the backbone torsion angles and the glycosidic orientation. Sequence-dependent conformational variations of the type observed here may contribute to the specificity of certain protein-DNA interactions.
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[[Category: Rabinovich D]]
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[[Category: Salisbury SA]]
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==About this Structure==
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[[Category: Shakked Z]]
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1VJ4 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=1VJ4 OCA].
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[[Category: Viswamitra MA]]
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==Reference==
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Sequence-dependent conformation of an A-DNA double helix. The crystal structure of the octamer d(G-G-T-A-T-A-C-C)., Shakked Z, Rabinovich D, Kennard O, Cruse WB, Salisbury SA, Viswamitra MA, J Mol Biol. 1983 May 15;166(2):183-201. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/6854642 6854642]
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[[Category: Protein complex]]
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[[Category: Cruse, W B.]]
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[[Category: Kennard, O.]]
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[[Category: Rabinovich, D.]]
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[[Category: Salisbury, S A.]]
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[[Category: Shakked, Z.]]
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[[Category: Viswamitra, M A.]]
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[[Category: a-dna]]
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[[Category: double helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:46:18 2008''
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Current revision

SEQUENCE-DEPENDENT CONFORMATION OF AN A-DNA DOUBLE HELIX: THE CRYSTAL STRUCTURE OF THE OCTAMER D(G-G-T-A-T-A-C-C)

PDB ID 1vj4

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