1M6R

Crystal structure of rGd(CGCGCG) forming hexamer Z-DNA duplex with 5'-(rG) overhang

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2002-07-17 Released: 2003-02-25 
  • Deposition Author(s): Pan, B., Sundaralingam, M.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of rGd(CGCGCG): a Z-DNA hexamer duplex with a 5'-(rG) overhang.

Pan, B.Sundaralingam, M.

(2003) Acta Crystallogr D Biol Crystallogr 59: 433-437

  • DOI: 10.1107/s0907444902022655
  • Primary Citation of Related Structures:  
    1M6R

  • PubMed Abstract: 
  • The crystal structure of the heptamer rGd(CGCGCG) has been determined at 1.54 A resolution with R(work) and R(free) of 0.191 and 0.235, respectively. The crystal belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 17.96, b = 31.47, c ...

    The crystal structure of the heptamer rGd(CGCGCG) has been determined at 1.54 A resolution with R(work) and R(free) of 0.191 and 0.235, respectively. The crystal belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 17.96, b = 31.47, c = 44.73 A and two independent strands in the asymmetric unit. The chimera forms a Z-DNA hexamer duplex d(CGCGCG)(2), with the 5'-overhang rG invisible in the density. The replacement of rG in the 5' terminus of d(GCGCGCG) changes the reverse Hoogsteen G.G base pairing of the 5'-overhang dG (Pan et al., 1997). However, the replacement does not change the helix from Z-form to A-form or the water-structure motifs in the Z-DNA double-helical structure.


    Organizational Affiliation

    Departments of Chemistry and Biochemistry, 200 Johnston Laboratory, 176 West 19th Avenue, Columbus, Ohio 43210-1002, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-R(*G)D(*CP*GP*CP*GP*CP*G)-3'A, B7N/A
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.54 Å
    • R-Value Free: 0.191 
    • R-Value Work: 0.162 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 17.96α = 90
    b = 31.47β = 90
    c = 44.73γ = 90
    Software Package:
    Software NamePurpose
    CNSrefinement

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2003-02-25
      Type: Initial release
    • Version 1.1: 2008-04-28
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2017-10-11
      Changes: Refinement description