1D90

REFINED CRYSTAL STRUCTURE OF AN OCTANUCLEOTIDE DUPLEX WITH I.T MISMATCHED BASE PAIRS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Observed: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Refined crystal structure of an octanucleotide duplex with I.T. mismatched base pairs.

Cruse, W.B.Aymani, J.Kennard, O.Brown, T.Jack, A.G.Leonard, G.A.

(1989) Nucleic Acids Res 17: 55-72

  • DOI: 10.1093/nar/17.1.55
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The structure of the synthetic deoxyoctamer d(GGIGCTCC) has been determined by single crystal X-ray diffraction techniques to a resolution of 1.7A. The sequence crystallises in space group P6(1), with unit cell dimensions a = b = 45.07, c = 45.49A. T ...

    The structure of the synthetic deoxyoctamer d(GGIGCTCC) has been determined by single crystal X-ray diffraction techniques to a resolution of 1.7A. The sequence crystallises in space group P6(1), with unit cell dimensions a = b = 45.07, c = 45.49A. The refinement converged with a crystallographic residual R = 0.14 and the location of 81 solvent molecules. The octamer forms an A-DNA duplex with 6 Watson-Crick (G.C) base pairs and 2 inosine-thymine (I.T) pairs. Refinement of the structure shows it to be essentially isomorphous with that reported for d(GGGGCTCC) with the mispairs adopting a "wobble" conformation. Conformational parameters and base stacking interactions are compared to those for the native duplex d(GGGGCCCC) and other similar sequences. A rationale for the apparent increased crystal packing efficiency and lattice stability of the I.T octamer is given.


    Organizational Affiliation

    University Chemical Laboratory, Cambridge, UK.



Macromolecules
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*IP*GP*CP*TP*CP*C)-3')A, B8N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Observed: 0.140 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.07α = 90
b = 45.07β = 90
c = 45.49γ = 120
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-07-15
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance