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: 1.8 Å

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This is version 1.2 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


  • 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 ...

    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



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*GP*TP*AP*TP*AP*CP*C)-3'A,B8N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 44.970α = 90.00
b = 44.970β = 90.00
c = 41.756γ = 120.00
Software Package:
Software NamePurpose
CORELSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1989-01-11
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance