9DNA

CRYSTAL STRUCTURE ANALYSIS OF AN A-DNA FRAGMENT AT 1.8 ANGSTROMS RESOLUTION. D(GCCCGGGC)

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 1987-07-10 Released: 1988-01-16 
  • Deposition Author(s): Heinemann, U.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.171 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure analysis of an A-DNA fragment at 1.8 A resolution: d(GCCCGGGC).

Heinemann, U.Lauble, H.Frank, R.Blocker, H.

(1987) Nucleic Acids Res 15: 9531-9550

  • DOI: 10.1093/nar/15.22.9531
  • Primary Citation of Related Structures:  
    9DNA

  • PubMed Abstract: 
  • Single crystals of the self-complementary octadeoxyribonucleotide d(GCCCGGGC) have been analysed by X-ray diffraction methods at a resolution of 1.8 A. The tetragonal unit cell of space group P4(3)2(1)2 has dimensions of a = 43.25 A and c = 24.61 A and contains eight strands of the oligonucleotide ...

    Single crystals of the self-complementary octadeoxyribonucleotide d(GCCCGGGC) have been analysed by X-ray diffraction methods at a resolution of 1.8 A. The tetragonal unit cell of space group P4(3)2(1)2 has dimensions of a = 43.25 A and c = 24.61 A and contains eight strands of the oligonucleotide. The structure was refined by standard crystallographic techniques to an R factor of 17.1% using 1359 3 sigma structure factor observations. Two strands of the oligonucleotide are related by the crystallographic dyad axis to form a DNA helix in the A conformation. The d(GCCCGGGC) helix is characterized by a wide open major groove, a near perpendicular orientation of base pairs to the helix axis and an unusually small average helix twist angle of 31.3 degrees indicating a slightly underwound helix with 11.5 base pairs per turn. Extensive cross-strand stacking between guanine bases at the central cytosine-guanine step is made possible by a number of local conformational adjustments including a fully extended sugar-phosphate backbone of the central guanosine nucleotide.


    Organizational Affiliation

    Abteilung Saenger, Freie Universität Berlin, FRG.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*CP*CP*CP*GP*GP*GP*C)-3')A8N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.171 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.25α = 90
b = 43.25β = 90
c = 24.61γ = 90
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1988-01-16
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance