1VT6

Molecular structure of the octamer D(G-G-C-C-G-G-C-C) modified A-DNA

• PDB DOI: https://doi.org/10.2210/pdb1VT6/pdb
• NAKB: 1VT6

• Classification: DNA
• Mutation(s): No 


• Deposited: 1988-08-18 Released: 2011-07-13 
• Deposition Author(s): Wang, A.H.-J., Fujii, S., Van Boom, J.H., Rich, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Work: 0.174 
• R-Value Observed: 0.174 

Literature

Molecular structure of the octamer d(G-G-C-C-G-G-C-C): modified A-DNA.

Wang, A.H., Fujii, S., van Boom, J.H., Rich, A.

(1982) Proc Natl Acad Sci U S A 79: 3968-3972

• PubMed: 6955784 
• DOI: https://doi.org/10.1073/pnas.79.13.3968
• Primary Citation of Related Structures:  
  1VT6


• PubMed Abstract: 
  

  The deoxynucleotide fragment d(GpGpCpCpGpGpCpC) was synthesized and crystallized, and its three-dimensional structure was determined by x-ray diffraction techniques to a resolution of 2.25 A. The molecule forms a right-handed double helix in which the two base pairs at either end of the molecule are in the conventional A-DNA conformation, while the central four base pairs have a modified form in which alternate residues have sugar conformations that are closer to those in B-DNA than in A-DNA. The molecules have an intermolecular contact in which the planar terminal guanine . cytosine base pair lies on the flat minor groove surface of the A-DNA helix.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 2.43 kDa 
• Atom Count: 161 
• 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*CP*CP*GP*GP*CP*C)-3')	A	8	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Work: 0.174 
• R-Value Observed: 0.174 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.06	α = 90
b = 42.06	β = 90
c = 25.17	γ = 90

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-13 
Deposition Author(s): Wang, A.H.-J., Fujii, S., Van Boom, J.H., Rich, A.

Revision History  

• Version 1.0: 2011-07-13
  Type: Initial release
  
• Version 1.1: 2023-12-27
  Changes: Data collection, Database references