1NDN | pdb_00001ndn

MOLECULAR STRUCTURE OF NICKED DNA. MODEL T4

• PDB DOI: https://doi.org/10.2210/pdb1NDN/pdb
• NAKB: 1NDN

• Classification: DNA
• Mutation(s): No 


• Deposited: 1992-01-15 Released: 1992-07-14 
• Deposition Author(s): Aymani, J., Coll, M., Van Der Marel, G.A., Van Boom, J.H., Wang, A.H.-J., Rich, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Observed: 
  0.186 (Depositor) 

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 U S A 87: 2526-2530

• PubMed: 2320572 
• DOI: https://doi.org/10.1073/pnas.87.7.2526
• Primary Citation of Related Structures:  
  1NDN, 1VTE


• 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-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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 7.28 kDa 
• Atom Count: 544 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*AP*CP*GP*CP*G)-3')	A	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*GP*TP*T)-3')	B	6	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*CP*GP*CP*G)-3')	C	6	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.99	α = 90
b = 44.03	β = 90
c = 66.62	γ = 90

Software Package:

Software Name	Purpose
ULTIMA	model building
NUCLSQ	refinement
ULTIMA	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1992-07-14 
Deposition Author(s): Aymani, J., Coll, M., Van Der Marel, G.A., Van Boom, J.H., Wang, A.H.-J., Rich, A.

Revision History  

• Version 1.0: 1992-07-14
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references