3FT6 | pdb_00003ft6

Crystal Structure of Proflavine in Complex with a DNA hexamer duplex

• PDB DOI: https://doi.org/10.2210/pdb3FT6/pdb
• NAKB: 3FT6

• Classification: DNA
• Mutation(s): No 


• Deposited: 2009-01-12 Released: 2010-02-02 
• Deposition Author(s): Maehigashi, T., Persil, O., Hud, N.V., Williams, L.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free: 
  0.219 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.184 (Depositor) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Proflavine in Complex with a DNA hexamer duplex

Maehigashi, T., Persil, O., Hud, N.V., Williams, L.D.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 4.52 kDa 
• Atom Count: 330 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*AP*TP*CP*G)-3'	A, B	6	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRL	C [auth A], F [auth B]	PROFLAVIN C13 H11 N3 WDVSHHCDHLJJJR-UHFFFAOYSA-N
NCO	D [auth A], E [auth A], G [auth B]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free:  0.219 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.184 (Depositor) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.563	α = 90
b = 24.563	β = 90
c = 78.276	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-02 
Deposition Author(s): Maehigashi, T., Persil, O., Hud, N.V., Williams, L.D.

Revision History  

• Version 1.0: 2010-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description