1D92

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Observed: 0.136 

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 G . T mismatched base-pairs.

Hunter, W.N.Kneale, G.Brown, T.Rabinovich, D.Kennard, O.

(1986) J Mol Biol 190: 605-618

  • DOI: 10.1016/0022-2836(86)90246-9
  • Primary Citation of Related Structures:  
    1D92

  • PubMed Abstract: 
  • Single crystal X-ray diffraction techniques have been used to determine the structure of the DNA octamer d(G-G-G-G-C-T-C-C) at a resolution of 2.25 A. The asymmetric unit consists of two strands coiled about each other to produce an A-type DNA helix. The double helix contains six G ...

    Single crystal X-ray diffraction techniques have been used to determine the structure of the DNA octamer d(G-G-G-G-C-T-C-C) at a resolution of 2.25 A. The asymmetric unit consists of two strands coiled about each other to produce an A-type DNA helix. The double helix contains six G . C Watson-Crick base-pairs and two G . T mismatched base-pairs. The mismatches adopt a "wobble" type structure in which both bases retain their major tautomer forms. The double helix is able to accommodate this G . T pairing with little distortion of the overall helical conformation. Crystals of this octamer melt at a substantially lower temperature than do those of a related octamer also containing two G . T base-pairs. We attribute this destabilization to disruption of the hydration network around the mismatch site combined with changes in intermolecular packing. Full details are given of conformational parameters, base stacking, intermolecular contacts and hydration involving 52 solvent molecules.


    Related Citations: 
    • High-Resolution Structure of a DNA Helix Containing Mismatched Base Pairs
      Brown, T., Kennard, O., Kneale, G., Rabinovich, D.
      (1985) Nature 315: 604
    • Structural Studies of DNA Fragments. The G.T Wobble Base Pair in A, B and Z DNA. The G.A Base Pair in B-DNA
      Kennard, O.
      (1985) J Biomol Struct Dyn 3: 205

    Organizational Affiliation

    Structural Biology Center, Korea Institute of Science and Technology (KIST), Cheongryang Box 131, Seoul, 130-650, Korea.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*GP*GP*GP*CP*TP*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: 2.25 Å
    • R-Value Observed: 0.136 
    • Space Group: P 61
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 45.2α = 90
    b = 45.2β = 90
    c = 42.97γ = 120
    Software Package:
    Software NamePurpose
    NUCLSQrefinement

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • 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