4OKL | pdb_00004okl

Crystal Structure of d(CCCCGGTACCGGGG)2 at 1.65 Angstrom

• PDB DOI: https://doi.org/10.2210/pdb4OKL/pdb
• NAKB: 4OKL

• Classification: DNA
• Mutation(s): No 


• Deposited: 2014-01-22 Released: 2014-02-19 
• Deposition Author(s): Anna, V., Monica, P., Mandal, P.K., Gautham, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.242 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Structure of d(CCCCGGTACCGGGG)2 at 1.65 angstrom resolution.

Purushothaman, M., Varghese, A., Mandal, P.K., Gautham, N.

(2014) Acta Crystallogr Sect F Struct Biol Cryst Commun 70: 860-865

• PubMed: 25005078 
• DOI: https://doi.org/10.1107/S2053230X1401084X
• Primary Citation Related Structures: 
  4OKL


• PubMed Abstract: 
  

  The crystal structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 has previously been reported as an A-type double helix at a resolution of 2.5 Å in space group P41. Here, the structure of this sequence was determined at a significantly higher resolution of 1.65 Å in space group P4₁2₁2. The differences in crystal packing between the former and latter are described. The crystallographic asymmetric unit consists of one tetradecanucleotide duplex that spans more than one full turn of the A-helix. This structure allowed the unambiguous identification of solvent interactions.

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Organizational Affiliation: 
• CAS in Crystallography and Biophysics, University of Madras, Guindy, Chennai, Tamil Nadu 600 025, India.
Institut Européen de Chimie et Biologie (IECB), 2 Rue Robert Escarpit, 33607 Pessac CEDEX, France.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 8.57 kDa 
• Atom Count: 613 
• Modeled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
14 mer A-DNA	A, B	14	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.242 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.27	α = 90
b = 41.27	β = 90
c = 87.67	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
AMoRE	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-19 
Deposition Author(s): Anna, V., Monica, P., Mandal, P.K., Gautham, N.

Revision History  

• Version 1.0: 2014-02-19
  Type: Initial release
  
• Version 1.1: 2014-12-10
  Changes: Database references
• Version 1.2: 2020-10-21
  Changes: Data collection
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Refinement description