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: 1.50 Å
  • R-Value Work: 0.225 
  • R-Value Observed: 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

  • DOI: 10.1021/bi00120a035
  • Structures With Same Primary Citation

  • 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
    • 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 U S A 77: 4016
    • 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

    Organizational Affiliation

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



Macromolecules
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*IP*CP*IP*CP*G)-3')A, B2N/A
  • Find similar nucleic acids by: Sequence   |   Structure
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: 1.50 Å
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31α = 90
b = 31β = 90
c = 43.7γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement
NUCLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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