197D

ORTHORHOMBIC CRYSTAL STRUCTURE OF THE A-DNA OCTAMER D(GTACGTAC). COMPARISON WITH THE TETRAGONAL STRUCTURE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Orthorhombic crystal structure of the A-DNA octamer d(GTACGTAC). Comparison with the tetragonal structure.

Langlois d'Estaintot, B.Dautant, A.Courseille, C.Precigoux, G.

(1993) Eur J Biochem 213: 673-682

  • DOI: 10.1111/j.1432-1033.1993.tb17807.x
  • Primary Citation of Related Structures:  
    197D

  • PubMed Abstract: 
  • The X-ray crystal structure of the double-helical A-DNA octanucleotide d(GTACGTAC) has been solved by molecular replacement and refined to a resolution of 0.219 nm. The final R-factor is equal to 16.1% for 1516 observed reflections with F > 4 sigma(F). The sequence crystallizes as an A-DNA-type double helix in the orthorhombic space group P2(1)2(1)2, with one duplex molecule solvated by 66 water molecules in the asymmetric unit ...

    The X-ray crystal structure of the double-helical A-DNA octanucleotide d(GTACGTAC) has been solved by molecular replacement and refined to a resolution of 0.219 nm. The final R-factor is equal to 16.1% for 1516 observed reflections with F > 4 sigma(F). The sequence crystallizes as an A-DNA-type double helix in the orthorhombic space group P2(1)2(1)2, with one duplex molecule solvated by 66 water molecules in the asymmetric unit. Cell parameters are a = 3.860 nm, b = 5.082 nm, c = 2.174 nm. It is the first time that such a crystal form has been observed. This orthorhombic structure has been compared with the tetragonal structure of the same oligonucleotide. It adopts a bent structure with an unusual packing between symmetry-related molecules.


    Related Citations: 
    • Crystal Structure Analysis of an A(DNA) Octamer d(GTACGTAC)
      Courseille, C., Dautant, A., Hospital, M., Langlois D'Estaintot, B., Precigoux, G., Molko, D., Teoule, R.
      (1990) Acta Crystallogr A 46: 9

    Organizational Affiliation

    Laboratoire de Cristallographie et de Physique Cristalline, Unité de Recherche Associée 144, Centre National de la Recherche Scientifique, Université de Bordeaux I, France.



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

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.19 Å
    • R-Value Observed: 0.161 
    • Space Group: P 21 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 38.605α = 90
    b = 50.824β = 90
    c = 21.74γ = 90
    Software Package:
    Software NamePurpose
    NUCLSQrefinement

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1995-02-07
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance