243D | pdb_0000243d

STRUCTURE OF THE DNA OCTANUCLEOTIDE D(ACGTACGT)2

• PDB DOI: https://doi.org/10.2210/pdb243D/pdb
• NAKB: 243D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1996-01-10 Released: 1996-02-26 
• Deposition Author(s): Wilcock, D.J., Adams, A., Cardin, C.J., Wakelin, L.P.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Work: 
  0.177 (Depositor) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Structure of the DNA octanucleotide d(ACGTACGT)2.

Wilcock, D.J., Adams, A., Cardin, C.J., Wakelin, L.P.

(1996) Acta Crystallogr D Biol Crystallogr 52: 481-485

• PubMed: 15299669 
• DOI: https://doi.org/10.1107/S0907444995016052
• Primary Citation Related Structures: 
  243D


• PubMed Abstract: 
  

  d(ACGTACGT), C(78)H(84)N(30)O(32)P(7).20H(2)O, M(r) (DNA) = 2170, tetragonal, P4(3)2(1)2 (No 96), a = 42.845 (1), b = 42.845(1), c = 24.804 (1) A, V = 45532.5 (2) A(3), z = 8,lambda(MoKalpha) = 0.71069 A, micro (MoKalpha) = 0.10 mm(-1), T = 295 K, R = 0.18 for 1994 unique reflections between 5.0 and 1.9 A resolution. The self-complementary octanucleotide d(ACGTACGT)(2) has been crystallized and its structure determined to a resolution of 1.9 A. The asymmetric unit consists of a single strand of octamer with 20 water molecules. It is only the second example of an octanucleotide having terminal A.T base pairs whose structure has been determined by X-ray crystallography. The sequence adopts the modified A-type conformation found for all octanucleotide duplexes studied to date with the helix bent by approximately 15 degrees and an average tilt angle of 0 degrees. Unusually the data collection was carried out using a 3 kW molybdenum sealed-tube source. The conformational details are discussed in comparison with other closely related sequences.

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Organizational Affiliation: 
• Department of Chemistry, Trinity College, Dublin, Ireland.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.43 kDa 
• Atom Count: 181 
• Modeled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3')	A	8	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Work:  0.177 (Depositor) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.845	α = 90
b = 42.845	β = 90
c = 24.804	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-02-26 
Deposition Author(s): Wilcock, D.J., Adams, A., Cardin, C.J., Wakelin, L.P.G.

Revision History  

• Version 1.0: 1996-02-26
  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: 2018-04-04
  Changes: Data collection
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references