1BNA

STRUCTURE OF A B-DNA DODECAMER. CONFORMATION AND DYNAMICS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a B-DNA dodecamer: conformation and dynamics.

Drew, H.R.Wing, R.M.Takano, T.Broka, C.Tanaka, S.Itakura, K.Dickerson, R.E.

(1981) Proc Natl Acad Sci U S A 78: 2179-2183

  • DOI: 10.1073/pnas.78.4.2179
  • Primary Citation of Related Structures:  
    1BNA

  • PubMed Abstract: 
  • The crystal structure of the synthetic DNA dodecamer d(CpGpCpGpApApTpTpCpGpCpG) has been refined to a residual error of R = 17.8% at 1.9-A resolution (two-sigma data). The molecule forms slightly more than one complete turn of right-handed double-str ...

    The crystal structure of the synthetic DNA dodecamer d(CpGpCpGpApApTpTpCpGpCpG) has been refined to a residual error of R = 17.8% at 1.9-A resolution (two-sigma data). The molecule forms slightly more than one complete turn of right-handed double-stranded B helix. The two ends of the helix overlap and interlock minor grooves with neighboring molecules up and down a 2(1) screw axis, producing a 19 degrees bend in helix axis over the 11-base-pair steps of the dodecamer. In the center of the molecule, where perturbation is least, the helix has a mean rotation of 36.9 degrees per step, or 9.8 base pairs per turn. The mean propeller twist (total dihedral angle between base planes) between A . T base pairs in the center of the molecule is 17.3 degrees, and that between C . G pairs on the two ends averages 11.5 degrees. Individual deoxyribose ring conformations as measured by the C5'-C4'-C3'-O3' torsion angle delta, exhibit an approximately Gaussian distribution centered around the C1'-exo position with delta avg = 123 degrees and a range of 79 degrees to 157 degrees. Purine sugars cluster at high delta values, and pyrimidine sugars cluster at lower delta. A tendency toward 2-fold symmetry in sugar conformation about the center of the molecule is detectable in spite of the destruction of ideal 2-fold symmetry by the molecular bending. More strikingly, sugar conformations of paired based appear to follow a "principle of anticorrelation," with delta values lying approximately the same distance to either side of the center value, delta = 123 degrees. This same anticorrelation is also observed in other DNA and DNA . RNA structures.


    Related Citations: 
    • Kinematic Model for B-DNA
      Dickerson, R.E., Drew, H.R.
      (1981) Proc Natl Acad Sci U S A 78: 7318
    • Structure of a B-DNA Dodecamer. II. Influence of Base Sequence on Helix Structure
      Dickerson, R.E., Drew, H.R.
      (1981) J Mol Biol 149: 761
    • Structure of a B-DNA Dodecamer. III. Geometry of Hydration
      Drew, H.R., Dickerson, R.E.
      (1981) J Mol Biol 151: 535
    • Crystal Structure Analysis of a Complete Turn of B-DNA
      Wing, R., Drew, H.R., Takano, T., Broka, C., Tanaka, S., Itakura, K., Dickerson, R.E.
      (1980) Nature 287: 755

    Organizational Affiliation

    Next Generation Healthcare Innovation Center, Fujitsu Limited, 17-25, Shinkamata 1-chome, Ota-ku, Tokyo, Tokyo 144-8588, Japan.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')A, B12N/A
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.90 Å
    • R-Value Observed: 0.178 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 24.87α = 90
    b = 40.39β = 90
    c = 66.2γ = 90
    Software Package:
    Software NamePurpose
    JACK-LEVITTrefinement

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 1981-05-21
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance