5BOK | pdb_00005bok

Ferredoxin component of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2

• PDB DOI: https://doi.org/10.2210/pdb5BOK/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Diaphorobacter sp. DS2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-27 Released: 2016-07-27 
• Deposition Author(s): Ramaswamy, S., Kumari, A., Singh, D., Gurunath, R.
• Funding Organization(s): Department of biotechnology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Ferredoxin component of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2

Ramaswamy, S., Kumari, A., Singh, D., Qurunath, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.72 kDa 
• Atom Count: 816 
• Modeled Residue Count: 102 
• Deposited Residue Count: 104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferredoxin	A	104	Diaphorobacter sp. DS2	Mutation(s): 0  Gene Names: mntAb

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES	B [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
FE	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.53	α = 90
b = 79.53	β = 90
c = 108.97	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
d*TREK	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-07-27 
Deposition Author(s): Ramaswamy, S., Kumari, A., Singh, D., Gurunath, R.

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Funding Organization	Location	Grant Number
Department of biotechnology	India	--

Revision History  

• Version 1.0: 2016-07-27
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description