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HELIX GEOMETRY AND HYDRATION IN AN A-DNA TETRAMER. IC-C-G-G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Helix geometry and hydration in an A-DNA tetramer: IC-C-G-G

Conner, B.N.Yoon, C.Dickerson, J.L.Dickerson, R.E.

(1984) J.Mol.Biol. 174: 663-695


  • PubMed Abstract: 
  • The DNA oligomer of sequence IC-C-G-G has been synthesized, and its X-ray crystal structure solved at a resolution of 2.0 A, using anomalous scattering from iodines in phase analysis: 48 cycles of Jack-Levitt restrained least-squares refinement resul ...

    The DNA oligomer of sequence IC-C-G-G has been synthesized, and its X-ray crystal structure solved at a resolution of 2.0 A, using anomalous scattering from iodines in phase analysis: 48 cycles of Jack-Levitt restrained least-squares refinement resulted in a residual error of 19.9% over all data, or 16.5% for two-sigma data. Two double-helical tetramers stack in the crystal to form a continuous octamer, except for the two missing phosphate connections across the center. The octamer has a mean helix rotation of 33.7 degrees (10.7 base-pairs per turn), rise of 2.87 A, mean inclination angle of base-pairs of 14 degrees, and mean base-pair propeller twist of +16.3 degrees. Local variations in both helix rotation and base plane roll angles, including those across the center of the octamer, are as predicted from base sequence by sum functions sigma 1 and sigma 2. The three known DNA octamers: IC-C-G-G/IC-C-G-G, G-G-T-A-T-A-C-C and G-G-C-C-G-G-C-C, make up a graded series in this order, with monotonically changing structural parameters. An exhaustive comparison of torsion angle correlations among the known A helices confirms some structural expectations and reveals some new features. 86 water molecules have been located per double-helical IC-C-G-G tetramer (the asymmetric unit), of which 451/2 per tetramer lie within a first hydrogen-bonded shell of hydration. No ordered water structure is observed comparable to the minor groove spine of hydration in B-DNA.


    Related Citations: 
    • The Molecular Structure of d(ICpCpGpG), a Fragment of Right-Handed Double Helical A-DNA
      Conner, B.N.,Takano, T.,Tanaka, S.,Itakura, K.,Dickerson, R.E.
      (1982) Nature 295: 294



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*(C38)P*CP*GP*G)-3')A,B4N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
C38
Query on C38
A, B
DNA LINKINGC9 H13 I N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 41.100α = 90.00
b = 41.100β = 90.00
c = 26.700γ = 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: 1982-07-29
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance