232D

THE HIGH RESOLUTION CRYSTAL STRUCTURE OF THE DNA DECAMER D(AGGCATGCCT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The high resolution crystal structure of the DNA decamer d(AGGCATGCCT).

Nunn, C.M.Neidle, S.

(1996) J.Mol.Biol. 256: 340-351

  • DOI: 10.1006/jmbi.1996.0090

  • PubMed Abstract: 
  • The crystal structure of the DNA decamer d(AGGCATGCCT) has been determined to a resolution of 1.3 A and R factor of 13.9%. The structure has a unique conformation with each of the decamer single strands forming base-pairing interactions with two symm ...

    The crystal structure of the DNA decamer d(AGGCATGCCT) has been determined to a resolution of 1.3 A and R factor of 13.9%. The structure has a unique conformation with each of the decamer single strands forming base-pairing interactions with two symmetry-related strands. The central eight bases of the decamer form an A-DNA octamer duplex with one symmetry-related strand whilst the terminal 5'-A and T-3' bases are flipped out and away from the octamer helix axis to form base-pairing interactions with a second symmetry-related strand. These A.T base-pairs lie perpendicular to the crystallographic c axis and pack within the unit cell in conjunction with a symmetry-related A.T base-pair displaced by 3.4 A degrees along the c axis. A novel base triplet interaction of the type A*(G.C) is present in the structure with interaction from the major groove side of the terminal 5'-A base to the minor groove of the central A-DNA octamer. This structure reports the first example of cobalt hexammine binding to a right-handed DNA duplex. The crystallographic asymmetric unit contains two cobalt hexammine ligands with one site in the major groove coordinating via hydrogen bonds to the 5'-AGG bases, and the second site located between DNA molecules and interacting with the oxygen atoms of phosphate groups.


    Related Citations: 
    • The Structure of Chain-linked DNA as a Possible Model for the Transcription Bubble
      Nunn, C.M.,Neidle, S.
      (1995) Nat.Struct.Mol.Biol. 2: 1060


    Organizational Affiliation

    The CRC Biomolecular Structure Unit, The Institute of Cancer Research, Sutton Surrey, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*GP*CP*AP*TP*GP*CP*CP*T)-3')A10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NCO
Query on NCO

Download SDF File 
Download CCD File 
A
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.216 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 32.700α = 90.00
b = 32.700β = 90.00
c = 78.700γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SHELXL-93refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1995-09-05 
  • Released Date: 1996-03-22 
  • Deposition Author(s): Nunn, C.M., Neidle, S.

Revision History 

  • Version 1.0: 1996-03-22
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance