2D94

THE CONFORMATION OF THE DNA DOUBLE HELIX IN THE CRYSTAL IS DEPENDENT ON ITS ENVIRONMENT

• PDB DOI: https://doi.org/10.2210/pdb2D94/pdb
• NAKB: 2D94

• Classification: DNA
• Mutation(s): No 


• Deposited: 1993-07-13 Released: 1994-01-15 
• Deposition Author(s): Shakked, Z., Guerstein-Guzikevich, G., Eisenstein, M., Frolow, F., Rabinovich, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Observed: 0.162 

Literature

The conformation of the DNA double helix in the crystal is dependent on its environment.

Shakked, Z., Guerstein-Guzikevich, G., Eisenstein, M., Frolow, F., Rabinovich, D.

(1989) Nature 342: 456-460

• PubMed: 2586615 
• DOI: https://doi.org/10.1038/342456a0
• Primary Citation of Related Structures:  
  1VT8, 2D94


• PubMed Abstract: 
  

  Studies of the crystal structures of more than 30 synthetic DNA fragments have provided structural information about three basic forms of the double helix: A-, B- and Z-form DNA. These studies have demonstrated that the DNA double helix adopts a highly variable structure which is related to its base sequence. The extent to which such observed structures are influenced by the crystalline environment can be found by studying the same molecule in different crystalline forms. We have recently crystallized one particular oligomer in various crystal forms. Here we report the results of structural analyses of the different crystal structures and demonstrate that the DNA double helix can adopt a range of conformations in the crystalline state depending on hydration, molecular packing and temperature. These results have implications on our understanding of the influence of the environment on DNA structure, and on the modes of DNA recognition by proteins.

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Organizational Affiliation: 

Department of Structural Chemistry, Weizmann Institute of Science, Rehovot, Israel.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2.43 kDa 
• Atom Count: 249 
• Modelled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Observed: 0.162 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.28	α = 90
b = 43.28	β = 90
c = 24.66	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-15 
Deposition Author(s): Shakked, Z., Guerstein-Guzikevich, G., Eisenstein, M., Frolow, F., Rabinovich, D.

Revision History  

• Version 1.0: 1994-01-15
  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: 2018-04-18
  Changes: Data collection
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references