1UE3

Crystal structure of d(GCGAAAGC) containing hexaamminecobalt


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of d(GCGAAAGC) (hexagonal form): a base-intercalated duplex as a stable structure.

Sunami, T.Kondo, J.Hirao, I.Watanabe, K.Miura, K.I.Takenaka, A.

(2004) Acta Crystallogr D Biol Crystallogr 60: 90-96

  • DOI: 10.1107/s0907444903024703
  • Primary Citation of Related Structures:  
    1UE3, 1UE2

  • PubMed Abstract: 
  • A DNA fragment d(GCGAAAGC), postulated to adopt a stable mini-hairpin structure on the basis of its extraordinary properties, has been X-ray analyzed. Two octamers related by a crystallographic twofold symmetry are aligned in an antiparallel fashion and associate to form a duplex, which is maintained by two Watson-Crick G ...

    A DNA fragment d(GCGAAAGC), postulated to adopt a stable mini-hairpin structure on the basis of its extraordinary properties, has been X-ray analyzed. Two octamers related by a crystallographic twofold symmetry are aligned in an antiparallel fashion and associate to form a duplex, which is maintained by two Watson-Crick G.C base pairs and a subsequent sheared G.A pair at both ends. The central two A residues are free from base-pair formation. The corresponding base moieties of the two strands are intercalated and stacked on each other, forming a long column of G(1)-C(2)-G(3)-A(4)-A(5)(*)-A(5)-A(4)(*)-G(3)(*)-C(2)(*)-G(1)(*) (asterisks indicate the counter-strand). The Watson-Crick and major-groove sites of the four stacked adenine bases are exposed to the solvent region, suggesting a functional role. Since this structural motif is similar to those found in the nonamers d(G(Br)CGAAAGCT) and d(G(I)CGAAAGCT), the base-intercalated duplex may be a stable form of the specific sequence. Electrophoresis results suggest that the octamer has two states, monomeric and dimeric, in solution depending on the Mg(2+) concentration. The present duplex is preferred under the crystallization conditions, which correspond to physiologically allowed conditions.


    Organizational Affiliation

    Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*CP*GP*AP*AP*AP*GP*C)-3'A8N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    NCO
    Query on NCO

    Download Ideal Coordinates CCD File 
    E [auth A]COBALT HEXAMMINE(III)
    Co H18 N6
    DYLMFCCYOUSRTK-FGTKAUEHAT
     Ligand Interaction
    CL
    Query on CL

    Download Ideal Coordinates CCD File 
    B [auth A]CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    C [auth A], D [auth A]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.15 Å
    • R-Value Free: 0.239 
    • R-Value Work: 0.227 
    • Space Group: P 63 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 37.373α = 90
    b = 37.373β = 90
    c = 64.587γ = 120
    Software Package:
    Software NamePurpose
    MOSFLMdata reduction
    SCALAdata scaling
    AMoREphasing
    CNSrefinement
    CCP4data scaling

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2004-01-13
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance