3BNA

REVERSIBLE BENDING AND HELIX GEOMETRY IN A B-DNA DODECAMER: CGCGAATTBRCGCG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Observed: 0.130 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG.

Fratini, A.V.Kopka, M.L.Drew, H.R.Dickerson, R.E.

(1982) J Biol Chem 257: 14686-14707

  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A double-helical B-DNA dodecamer has been analyzed by single crystal x-ray diffraction methods and refined independently in four variants: sequence CGCGAATTCGCG at 20 degrees C and at 16 K, and CGCGAATTBrCGCG in 60% methylpentanediol at 20 and at 7 d ...

    A double-helical B-DNA dodecamer has been analyzed by single crystal x-ray diffraction methods and refined independently in four variants: sequence CGCGAATTCGCG at 20 degrees C and at 16 K, and CGCGAATTBrCGCG in 60% methylpentanediol at 20 and at 7 degrees C. The first three forms show a 14-19 degrees bend in overall helix axis, but the fourth is straight and unbent. Detailed comparisons of the various forms have led to a better understanding of helix geometry and bending. Structural principles can be understood best if organized under four headings: 1) intrinsic geometry of the sugar rings, 2) stacking and relative motion of base pairs, 3) geometry of the connecting phosphate backbone, and 4) mechanics of bending in B-DNA. The observed bending is neither completely localized nor smooth and continuous, but an intermediate compromise that can be termed "annealed kinking."


    Related Citations: 
    • Ordered Water Structure around a B-DNA Dodecamer. A Quantitative Study
      Kopka, M.L., Fratini, A.V., Drew, H.R., Dickerson, R.E.
      (1983) J Mol Biol 163: 129
    • Structure of a B-DNA Dodecamer at 16 Kelvin
      Drew, H.R., Samson, S., Dickerson, R.E.
      (1982) Proc Natl Acad Sci U S A 79: 4040
    • 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. 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
    • 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., Takano, T., Broka, C., Tanaka, S., Itakura, K., Dickerson, R.E.
      (1980) Nature 287: 755

    Organizational Affiliation

    Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, D-13125 Berlin, Germany.



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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Observed: 0.130 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 24.71α = 90
b = 40.56β = 90
c = 65.62γ = 90
Software Package:
Software NamePurpose
JACK-LEVITTrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1982-04-15
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance