1NDN

MOLECULAR STRUCTURE OF NICKED DNA. MODEL T4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular structure of nicked DNA: a substrate for DNA repair enzymes.

Aymami, J.Coll, M.van der Marel, G.A.van Boom, J.H.Wang, A.H.Rich, A.

(1990) Proc.Natl.Acad.Sci.USA 87: 2526-2530


  • PubMed Abstract: 
  • The molecular structure of a nicked dodecamer DNA double helix, made of a ternary system containing d(CGCGAAAACGCG) + d(CGCGTT) + d(TTCGCG) oligonucleotides, has been determined by x-ray diffraction analysis at 3 A resolution. The molecule adopts a B ...

    The molecular structure of a nicked dodecamer DNA double helix, made of a ternary system containing d(CGCGAAAACGCG) + d(CGCGTT) + d(TTCGCG) oligonucleotides, has been determined by x-ray diffraction analysis at 3 A resolution. The molecule adopts a B-DNA conformation, not unlike those found in intact dodecamer DNA molecules crystallized in a somewhat different crystal lattice, despite a gap due to the absence of a phosphate group in the molecule. The helix has a distinct narrow minor groove near the center of the molecule at the AAAA region. This suggests that the internal stabilizing forces due to base stacking and hydrogen-bonding interactions are sufficient to overcome the loss of connectivity associated with the disruption of the covalent backbone of DNA.


    Related Citations: 
    • Molecular Structure of the Netropsin-d(CGCGATATCGCG) Complex. DNA Conformation in an Alternating AT Segment
      Coll, M.,Aymami, J.,Van Der Marel, G.A.,Van Boom, J.H.,Rich, A.,Wang, A.H.-J.
      (1989) Biochemistry 28: 310
    • A Bifurcated Hydrogen-Bonded Conformation in the d(*A(dot)*T) Base Pairs of the DNA Dodecamer d(CGCAAATTTGCG) and Its Complex With Distamycin
      Coll, M.,Frederick, C.A.,Wang, A.H.-J.,Rich, A.
      (1987) Proc.Natl.Acad.Sci.USA 84: 8385
    • Crystal Structure Analysis of a Complete Turn of B-DNA
      Wing, R.,Drew, H.,Takano, T.,Broka, C.,Tanaka, S.,Itakura, K.,Dickerson, R.E.
      (1980) Nature 287: 755


    Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*AP*CP*GP*CP*G)-3')A12N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*GP*TP*T)-3')B6N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*CP*GP*CP*G)-3')C6N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 25.990α = 90.00
b = 44.030β = 90.00
c = 66.620γ = 90.00
Software Package:
Software NamePurpose
ULTIMAmodel building
NUCLSQrefinement
ULTIMAphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1992-07-14
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance