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

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


  • 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. ...

    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: 
    • 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
    • High-Resolution Structure of a DNA Helix Containing Mismatched Base Pairs
      Brown, T.,Kennard, O.,Kneale, G.,Rabinovich, D.
      (1985) Nature 315: 604



Macromolecules

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 45.200α = 90.00
b = 45.200β = 90.00
c = 42.970γ = 120.00
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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