3BNA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å

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

  • Primary Citation of Related Structures:  

  • 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: 
    • Structure of a B-DNA Dodecamer at 16 Kelvin
      Drew, H.R.,Samson, S.,Dickerson, R.E.
      (1982) Proc.Natl.Acad.Sci.USA 79: 4040
    • 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
    • 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. 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
    • Kinematic Model for B-DNA
      Dickerson, R.E.,Drew, H.R.
      (1981) Proc.Natl.Acad.Sci.USA 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.USA 78: 2179



Macromolecules

Find similar proteins 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
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CBR
Query on CBR
A, B
DNA LINKINGC9 H13 Br N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 24.710α = 90.00
b = 40.560β = 90.00
c = 65.620γ = 90.00
Software Package:
Software NamePurpose
JACK-LEVITTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

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