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 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1107/s0907444903024703
  • Primary Citation of Related Structures:  
    1UE2, 1UE3

  • 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.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   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*GP*CP*GP*AP*AP*AP*GP*C)-3'8N/A
Sequence Annotations
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  • Reference Sequence
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

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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
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description