197D | pdb_0000197d

ORTHORHOMBIC CRYSTAL STRUCTURE OF THE A-DNA OCTAMER D(GTACGTAC). COMPARISON WITH THE TETRAGONAL STRUCTURE

• PDB DOI: https://doi.org/10.2210/pdb197D/pdb
• NAKB: 197D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1994-11-24 Released: 1995-02-07 
• Deposition Author(s): Langlois D'Estaintot, B., Dautant, A., Courseille, C., Precigoux, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Observed: 
  0.161 (Depositor) 

Literature

Orthorhombic crystal structure of the A-DNA octamer d(GTACGTAC). Comparison with the tetragonal structure.

Langlois d'Estaintot, B., Dautant, A., Courseille, C., Precigoux, G.

(1993) Eur J Biochem 213: 673-682

• PubMed: 8477741 
• DOI: https://doi.org/10.1111/j.1432-1033.1993.tb17807.x
• Primary Citation of Related Structures:  
  197D


• PubMed Abstract: 
  

  The X-ray crystal structure of the double-helical A-DNA octanucleotide d(GTACGTAC) has been solved by molecular replacement and refined to a resolution of 0.219 nm. The final R-factor is equal to 16.1% for 1516 observed reflections with F > 4 sigma(F). The sequence crystallizes as an A-DNA-type double helix in the orthorhombic space group P2(1)2(1)2, with one duplex molecule solvated by 66 water molecules in the asymmetric unit. Cell parameters are a = 3.860 nm, b = 5.082 nm, c = 2.174 nm. It is the first time that such a crystal form has been observed. This orthorhombic structure has been compared with the tetragonal structure of the same oligonucleotide. It adopts a bent structure with an unusual packing between symmetry-related molecules.

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Organizational Affiliation: 
• Laboratoire de Cristallographie et de Physique Cristalline, Unité de Recherche Associée 144, Centre National de la Recherche Scientifique, Université de Bordeaux I, France.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 4.85 kDa 
• Atom Count: 388 
• Modeled 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*TP*AP*CP*GP*TP*AP*C)-3')	A, B	8	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.605	α = 90
b = 50.824	β = 90
c = 21.74	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-02-07 
Deposition Author(s): Langlois D'Estaintot, B., Dautant, A., Courseille, C., Precigoux, G.

Revision History  

• Version 1.0: 1995-02-07
  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