2BNA

STRUCTURE OF A B-DNA DODECAMER AT 16 KELVIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a B-DNA dodecamer at 16 K.

Drew, H.R.Samson, S.Dickerson, R.E.

(1982) Proc.Natl.Acad.Sci.USA 79: 4040-4044


  • PubMed Abstract: 
  • The crystal structure of the B-DNA dodecamer C-G-C-G-A-A-T-T-C-G-C-G, previously solved and refined at room temperature (290 K), has been analyzed at 16 K (-257 degrees C). The end-to-end winding of the helix does not vary with temperature but remain ...

    The crystal structure of the B-DNA dodecamer C-G-C-G-A-A-T-T-C-G-C-G, previously solved and refined at room temperature (290 K), has been analyzed at 16 K (-257 degrees C). The end-to-end winding of the helix does not vary with temperature but remains constant at 10.1 base pairs per turn. Negatively charged phosphate groups throughout the structure do move closer together on cooling, however, probably because of increase in the dielectric constant of water as the temperature is lowered. This has the two-fold effect of reducing the spacing between neighboring double helices from 24.0 to 22.9 A and of narrowing the helix grooves within any isolated molecule. Overall lattice displacements as deduced from crystallographic temperature factors are very much decreased in the 16 K structure, yet displacements at phosphates continue to exceed those of deoxyribose sugars by B = 9 A2 and those of base pairs by B = 22 A2, even at this very low temperature at which practically all thermal motion has been eliminated. These differences, formerly interpreted as evidence for thermal vibration, must now be attributed to static disorder.


    Related Citations: 
    • Structure of a B-DNA Dodecamer. III. Geometry of Hydration
      Drew, H.R.,Dickerson, R.E.
      (1981) J.Mol.Biol. 151: 535
    • 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
    • Kinematic Model for B-DNA
      Dickerson, R.E.,Drew, H.R.
      (1981) Proc.Natl.Acad.Sci.USA 78: 7318
    • 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
    • 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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
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: 2.7 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 23.440α = 90.00
b = 39.310β = 90.00
c = 65.260γ = 90.00
Software Package:
Software NamePurpose
JACK-LEVITTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1982-02-03
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance