243D

STRUCTURE OF THE DNA OCTANUCLEOTIDE D(ACGTACGT)2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the DNA octanucleotide d(ACGTACGT)2.

Wilcock, D.J.Adams, A.Cardin, C.J.Wakelin, L.P.

(1996) Acta Crystallogr.,Sect.D 52: 481-485

  • DOI: 10.1107/S0907444995016052

  • PubMed Abstract: 
  • d(ACGTACGT), C(78)H(84)N(30)O(32)P(7).20H(2)O, M(r) (DNA) = 2170, tetragonal, P4(3)2(1)2 (No 96), a = 42.845 (1), b = 42.845(1), c = 24.804 (1) A, V = 45532.5 (2) A(3), z = 8,lambda(MoKalpha) = 0.71069 A, micro (MoKalpha) = 0.10 mm(-1), T = 295 K, R ...

    d(ACGTACGT), C(78)H(84)N(30)O(32)P(7).20H(2)O, M(r) (DNA) = 2170, tetragonal, P4(3)2(1)2 (No 96), a = 42.845 (1), b = 42.845(1), c = 24.804 (1) A, V = 45532.5 (2) A(3), z = 8,lambda(MoKalpha) = 0.71069 A, micro (MoKalpha) = 0.10 mm(-1), T = 295 K, R = 0.18 for 1994 unique reflections between 5.0 and 1.9 A resolution. The self-complementary octanucleotide d(ACGTACGT)(2) has been crystallized and its structure determined to a resolution of 1.9 A. The asymmetric unit consists of a single strand of octamer with 20 water molecules. It is only the second example of an octanucleotide having terminal A.T base pairs whose structure has been determined by X-ray crystallography. The sequence adopts the modified A-type conformation found for all octanucleotide duplexes studied to date with the helix bent by approximately 15 degrees and an average tilt angle of 0 degrees. Unusually the data collection was carried out using a 3 kW molybdenum sealed-tube source. The conformational details are discussed in comparison with other closely related sequences.


    Organizational Affiliation

    Department of Chemistry, Trinity College, Dublin, Ireland.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3')A8N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.177 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 42.845α = 90.00
b = 42.845β = 90.00
c = 24.804γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-02-26
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance