5WV7

Crystal structure of d(CCGGGGTACCCCGG)2 at 1.4A resolution

• PDB DOI: https://doi.org/10.2210/pdb5WV7/pdb
• NAKB: 5WV7

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2016-12-22 Released: 2017-05-24 
• Deposition Author(s): Karthik, S., Thirugnanasambandam, A., Mandal, P.K., Gautham, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.242 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 

Literature

Crystal structure of d(CCGGGGTACCCCGG)2 at 1.4 angstrom resolution.

Karthik, S., Thirugnanasambandam, A., Mandal, P.K., Gautham, N.

(2017) Acta Crystallogr F Struct Biol Commun 73: 259-265

• PubMed: 28471357 
• DOI: https://doi.org/10.1107/S2053230X17004770
• Primary Citation of Related Structures:  
  5WV7


• PubMed Abstract: 
  

  The X-ray crystal structure of the DNA tetradecamer sequence d(CCGGGGTACCCCGG) ₂ is reported at 1.4 Å resolution in the tetragonal space group P4 ₁ 2 ₁ 2. The sequence was designed to fold as a four-way junction. However, it forms an A-type double helix in the presence of barium chloride. The metal ion could not be identified in the electron-density map. The crystallographic asymmetric unit consists of one A-type double helix with 12 base pairs per turn, in contrast to 11 base pairs per turn for canonical A-DNA. A large number of solvent molecules have been identified in both the grooves of the duplex and around the backbone phosphate groups.

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Organizational Affiliation: 

CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India.

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 8.57 kDa 
• Atom Count: 656 
• Modelled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*GP*GP*GP*TP*AP*CP*CP*CP*CP*GP*G)-3')	A, B	14	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.242 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 
• Space Group: P 4₁ 2₁ 2
• Diffraction Data: https://doi.org/10.5281/zenodo.2546683

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.803	α = 90
b = 41.803	β = 90
c = 89.33	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-24 
Deposition Author(s): Karthik, S., Thirugnanasambandam, A., Mandal, P.K., Gautham, N.

Revision History  

• Version 1.0: 2017-05-24
  Type: Initial release
  
• Version 1.1: 2019-01-30
  Changes: Data collection, Database references
• Version 1.2: 2019-11-20
  Changes: Data collection
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description