1VT5

THE CRYSTAL STRUCTURE OF D(CCCCGGGG): A NEW A-FORM VARIANT WITH AN EXTENDED BACKBONE CONFORMATION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The crystal structure of d(CCCCGGGG): a new A-form variant with an extended backbone conformation.

Haran, T.E.Shakked, Z.Wang, A.H.Rich, A.

(1987) J.Biomol.Struct.Dyn. 5: 199-217

  • DOI: 10.1080/07391102.1987.10506390

  • PubMed Abstract: 
  • The crystal structure of d(CCCCGGGG) has been determined at a resolution of 2.25 A. The oligomers crystallize as A-DNA duplexes occupying crystallographic two-fold axes. The backbone conformation is, in general, similar to that observed in previously ...

    The crystal structure of d(CCCCGGGG) has been determined at a resolution of 2.25 A. The oligomers crystallize as A-DNA duplexes occupying crystallographic two-fold axes. The backbone conformation is, in general, similar to that observed in previously reported crystal structures of A-DNA fragments, except for the central linkage, where it adopts an extended structure resulting from all trans conformation at the P-O5'-C5'-C4' bonds. This type of conformation facilitates interstrand stacking between the guanines at the C-G site. The local helix twist at this step is very small (25 degrees) compared to an overall average of 33.5 degrees. The unique structure of the C-G base-pair step, namely the extended backbone and the distinct stacking geometry, may be an important feature in the recognition mechanism between double-stranded DNA molecules and restriction endonucleases such as Msp I, which cuts the sequence CCGG very specifically with a rate unaffected by neighboring base pairs.


    Related Citations: 
    • Molecular structure of the octamer d(G-G-C-C-G-G-C-C): modified A-DNA.
      Wang, A.H.,Fujii, S.,van Boom, J.H.,Rich, A.
      (1982) Proc.Natl.Acad.Sci.USA 79: 3968


    Organizational Affiliation

    Dept. of Structural Chemistry, Weizmann Institute of Science, Rehovot,Israel.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*CP*CP*GP*GP*GP*G)-3')A8N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Work: 0.240 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 43.360α = 90.00
b = 43.360β = 90.00
c = 24.830γ = 90.00
Software Package:
Software NamePurpose
CORELSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-13
    Type: Initial release