1D90

REFINED CRYSTAL STRUCTURE OF AN OCTANUCLEOTIDE DUPLEX WITH I.T MISMATCHED BASE PAIRS

• PDB DOI: https://doi.org/10.2210/pdb1D90/pdb
• NAKB: 1D90

• Classification: DNA
• Mutation(s): No 


• Deposited: 1992-10-17 Released: 1993-07-15 
• Deposition Author(s): Cruse, W.B.T., Aymani, J., Kennard, O., Brown, T., Jack, A.G.C., Leonard, G.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Observed: 0.140 

Literature

Refined crystal structure of an octanucleotide duplex with I.T. mismatched base pairs.

Cruse, W.B., Aymani, J., Kennard, O., Brown, T., Jack, A.G., Leonard, G.A.

(1989) Nucleic Acids Res 17: 55-72

• PubMed: 2911488 
• DOI: https://doi.org/10.1093/nar/17.1.55
• Primary Citation of Related Structures:  
  1D90


• PubMed Abstract: 
  

  The structure of the synthetic deoxyoctamer d(GGIGCTCC) has been determined by single crystal X-ray diffraction techniques to a resolution of 1.7A. The sequence crystallises in space group P6(1), with unit cell dimensions a = b = 45.07, c = 45.49A. The refinement converged with a crystallographic residual R = 0.14 and the location of 81 solvent molecules. The octamer forms an A-DNA duplex with 6 Watson-Crick (G.C) base pairs and 2 inosine-thymine (I.T) pairs. Refinement of the structure shows it to be essentially isomorphous with that reported for d(GGGGCTCC) with the mispairs adopting a "wobble" conformation. Conformational parameters and base stacking interactions are compared to those for the native duplex d(GGGGCCCC) and other similar sequences. A rationale for the apparent increased crystal packing efficiency and lattice stability of the I.T octamer is given.

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Organizational Affiliation: 

University Chemical Laboratory, Cambridge, UK.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 4.86 kDa 
• Atom Count: 403 
• Modelled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*IP*GP*CP*TP*CP*C)-3')	A, B	8	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Observed: 0.140 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.07	α = 90
b = 45.07	β = 90
c = 45.49	γ = 120

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-07-15 
Deposition Author(s): Cruse, W.B.T., Aymani, J., Kennard, O., Brown, T., Jack, A.G.C., Leonard, G.A.

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