1D13

MOLECULAR STRUCTURE OF AN A-DNA DECAMER D(ACCGGCCGGT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular structure of an A-DNA decamer d(ACCGGCCGGT).

Frederick, C.A.Quigley, G.J.Teng, M.K.Coll, M.Van der Marel, G.A.Van Boom, J.H.Rich, A.Wang, A.H.

(1989) Eur.J.Biochem. 181: 295-307


  • PubMed Abstract: 
  • The molecular structure of the DNA decamer d(ACCGGCCGGT) has been solved and refined by single-crystal X-ray-diffraction analysis at 0.20 nm to a final R-factor of 18.0%. The decamer crystallizes as an A-DNA double helical fragment with unit-cell dim ...

    The molecular structure of the DNA decamer d(ACCGGCCGGT) has been solved and refined by single-crystal X-ray-diffraction analysis at 0.20 nm to a final R-factor of 18.0%. The decamer crystallizes as an A-DNA double helical fragment with unit-cell dimensions of a = b = 3.923 nm and c = 7.80 nm in the space group P6(1)22. The overall conformation of this A-DNA decamer is very similar to that of the fiber model for A-DNA which has a large average base-pair tilt and hence a wide and shallow minor groove. This structure is in contrast to that of several A-DNA octamers in which the molecules all have low base-pair-tilt angles (8-12 degrees) resulting in an appearance intermediate between B-DNA and A-DNA. The average helical parameters of this decamer are typical of A-DNA with 10.9 base pairs/turn of helix, an average helical twist angle of 33.1 degrees, and a base-pair-tilt angle of 18.2 degrees. However, the CpG step in this molecule has a low local-twist angle of 24.5 degrees, similar to that seen in other A-DNA oligomers, and therefore appears to be an intrinsic stacking pattern for this step. The molecules pack in the crystal using a recurring binding motif, namely, the terminal base pair of one helix abuts the surface of the shallow minor groove of another helix. In addition, the GC base pairs have large propeller-twist angles, unlike those found most other A-DNA structures.


    Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*CP*GP*GP*CP*CP*GP*GP*T)-3')A10N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 39.230α = 90.00
b = 39.230β = 90.00
c = 78.010γ = 120.00
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1990-10-15
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance