1VJ4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.198 

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This is version 1.3 of the entry. See complete history


Literature

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, W.B.Salisbury, S.A.Viswamitra, M.A.

(1983) J Mol Biol 166: 183-201

  • DOI: 10.1016/s0022-2836(83)80005-9
  • Primary Citation of Related Structures:  
    1VJ4

  • PubMed Abstract: 
  • 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 ...

    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.


    Related Citations: 
    • Crystalline A-DNA. The X-Ray Analysis of the Fragment d(G-G-T-A-T-A-C-C)
      Shakked, Z., Rabinovich, D., Cruse, W.B.T., Egert, E., Kennard, O., Sala, G., Salisbury, S.A., Viswamitra, M.A.
      (1981) Proc R Soc London,ser B 213: 479

    Organizational Affiliation

    Department of Chemical Sciences, Wyeth, CN 8000, Princeton, NJ 08543-8000, USA. malamas.michael@gmail.com



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*GP*TP*AP*TP*AP*CP*C)-3'A, B8N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.80 Å
    • R-Value Observed: 0.198 
    • Space Group: P 61
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 44.97α = 90
    b = 44.97β = 90
    c = 41.756γ = 120
    Software Package:
    Software NamePurpose
    CORELSrefinement

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1989-01-11
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2018-04-18
      Changes: Data collection