1D65 | pdb_00001d65

MOLECULAR STRUCTURE OF THE B-DNA DODECAMER D(CGCAAATTTGCG)2; AN EXAMINATION OF PROPELLER TWIST AND MINOR-GROOVE WATER STRUCTURE AT 2.2 ANGSTROMS RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1D65/pdb
• NAKB: 1D65

• Classification: DNA
• Mutation(s): No 


• Deposited: 1992-03-02 Released: 1993-01-15 
• Deposition Author(s): Edwards, K.J., Brown, D.G., Spink, N., Neidle, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 
  0.170 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Molecular structure of the B-DNA dodecamer d(CGCAAATTTGCG)2. An examination of propeller twist and minor-groove water structure at 2.2 A resolution.

Edwards, K.J., Brown, D.G., Spink, N., Skelly, J.V., Neidle, S.

(1992) J Mol Biology 226: 1161-1173

• PubMed: 1518049 
• DOI: https://doi.org/10.1016/0022-2836(92)91059-x
• Primary Citation of Related Structures:  
  1D65


• PubMed Abstract: 
  

  The crystal structure of the dodecanucleotide duplex d(CGCAAATTTGCG)2 has been solved to 2.2 A resolution and refined to an R-factor of 18.1% with the inclusion of 71 water molecules. The structure shows propeller twists of up to -20 degrees for the A.T base-pairs, although there is probably only one (weak) three-centre hydrogen bond in the six base-pair AT narrow minor-groove region. An extensive ribbon of hydration has been located in this groove that has features distinctive from the classic "spine of hydration". Solvation around phosphate groups is described, with several instances of water molecules bridging between phosphates.

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Organizational Affiliation: 

Cancer Research Campaign Biomolecular Structure Unit, Institute of Cancer Research, Sutton, Surrey, U.K.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.32 kDa 
• Atom Count: 557 
• 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*TP*GP*CP*G)-3')	A, B	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work:  0.170 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.87	α = 90
b = 40.9	β = 90
c = 65.64	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-01-15 
Deposition Author(s): Edwards, K.J., Brown, D.G., Spink, N., Neidle, S.

Revision History  

• Version 1.0: 1993-01-15
  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: 2024-02-07
  Changes: Data collection, Database references