111D

CRYSTAL STRUCTURE AND STABILITY OF A DNA DUPLEX CONTAINING A(ANTI).G(SYN) BASE-PAIRS

• PDB DOI: https://doi.org/10.2210/pdb111D/pdb
• NAKB: 111D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1993-01-04 Released: 1993-07-15 
• Deposition Author(s): Brown, T., Leonard, G.A., Booth, E.D., Chambers, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Observed: 0.160 

Literature

Crystal structure and stability of a DNA duplex containing A(anti).G(syn) base-pairs.

Brown, T., Leonard, G.A., Booth, E.D., Chambers, J.

(1989) J Mol Biol 207: 455-457

• PubMed: 2754734 
• DOI: https://doi.org/10.1016/0022-2836(89)90268-4
• Primary Citation of Related Structures:  
  111D


• PubMed Abstract: 
  

  The synthetic dodecanucleotide d(CGCAAATTGGCG) has been analysed by single-crystal X-ray diffraction techniques and the structure refined to R = 0.16 and 2.25 A resolution, with the location of 94 solvent molecules. The sequence crystallizes as a full turn of a B-DNA helix with ten Watson-Crick base-pairs and two adenine-guanine mispairs. The analysis clearly shows that the mismatches are of the form A(anti).G(syn). Thermal denaturation studies indicate that the stability of the duplex is strongly pH dependent, with a maximum at pH 5.0, suggesting that the base-pair is stabilized by protonation. Three different arrangements have been observed for base-pairs between guanine and adenine and it is likely that A.G mismatch conformation is strongly influenced by dipole-dipole interactions with adjacent base-pairs.

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Organizational Affiliation: 

Department of Chemistry, University of Edinburgh, U.K.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.37 kDa 
• Atom Count: 552 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Observed: 0.160 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.23	α = 90
b = 41.16	β = 90
c = 65.01	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-07-15 
Deposition Author(s): Brown, T., Leonard, G.A., Booth, E.D., Chambers, J.

Revision History  

• Version 1.0: 1993-07-15
  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: 2024-02-07
  Changes: Data collection, Database references