1D53

CRYSTAL STRUCTURE AT 1.5 ANGSTROMS RESOLUTION OF D(CGCICICG), AN OCTANUCLEOTIDE CONTAINING INOSINE, AND ITS COMPARISON WITH D(CGCG) AND D(CGCGCG) STRUCTURES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure at 1.5-A resolution of d(CGCICICG), an octanucleotide containing inosine, and its comparison with d(CGCG) and d(CGCGCG) structures.

Kumar, V.D.Harrison, R.W.Andrews, L.C.Weber, I.T.

(1992) Biochemistry 31: 1541-1550


  • PubMed Abstract: 
  • The octadeoxyribonucleotide d(CGCICICG) has been crystallized in space group P(6)5(22) with unit cell dimensions of a = b = 31.0 A and c = 43.7 A, and X-ray diffraction data have been collected to 1.5-A resolution. Precession photographs and the self ...

    The octadeoxyribonucleotide d(CGCICICG) has been crystallized in space group P(6)5(22) with unit cell dimensions of a = b = 31.0 A and c = 43.7 A, and X-ray diffraction data have been collected to 1.5-A resolution. Precession photographs and the self-Patterson function indicate that 12 base pairs of Z-conformation DNA stack along the c-axis, and the double helices pack in a hexagonal array similar to that seen in other crystals of Z-DNA. The structure has been solved by both Patterson deconvolution and molecular replacement methods and refined in space group P(6)5 to an R factor of 0.225 using 2503 unique reflections greater than 3.0 sigma (F). Comparison of the molecules within the hexagonal lattice with highly refined crystal structures of other Z-DNA reveals only minor conformational differences, most notably in the pucker of the deoxyribose of the purine residues. The DNA has multiple occupancy of C:I and C:G base pairs, and C:I base pairs adopt a conformation similar to that of C:G base pairs.


    Related Citations: 
    • The Molecular Structure of the Left-Handed Z-DNA Double Helix at 1.0 Angstrom Atomic Resolution. Geometry, Conformation, and Ionic Interaction of d(CGCGCG)
      Gessner, R.V.,Frederick, C.A.,Quigley, G.J.,Rich, A.,Wang, A.H.-J.
      (1989) J.Biol.Chem. 264: 7921
    • The Octamers d(CGCGCGCG) and d(CGCATGCG) Both Crystallize as Z-DNA in the Same Hexagonal Lattice
      Fujii, S.,Wang, A.H.-J.,Quigley, G.J.,Westerink, H.,Van Der Marel, G.,Van Boom, J.H.,Rich, A.
      (1985) Biopolymers 24: 243
    • High-Salt d(CpGpCpG), a Left-Handed Z'DNA Double Helix
      Drew, H.,Takano, T.,Tanaka, S.,Itakura, K.,Dickerson, R.
      (1980) Nature 286: 567
    • The Tetramer d(CpGpCpG) Crystallizes as a Left-Handed Double Helix
      Crawford, J.L.,Kolpak, F.J.,Wang, A.H.-J.,Quigley, G.J.,Van Boom, J.H.,Van Der Marel, G.,Rich, A.
      (1980) Proc.Natl.Acad.Sci.USA 77: 4016


    Organizational Affiliation

    National Cancer Institute, Frederick Cancer Research and Development Center, Maryland 21702-1201.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*IP*CP*IP*CP*G)-3')A,B2N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*G)-3')C,D4N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Work: 0.225 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 31.000α = 90.00
b = 31.000β = 90.00
c = 43.700γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
NUCLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-04-13
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance