3VB0

Crystal structure of 2,2',3-trihydroxybiphenyl 1,2-dioxygenase from dibenzofuran-degrading Sphingomonas wittichii strain RW1

• PDB DOI: https://doi.org/10.2210/pdb3VB0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhizorhabdus wittichii RW1
• Expression System: Pseudomonas putida
• Mutation(s): No 


• Deposited: 2011-12-30 Released: 2013-04-03 
• Deposition Author(s): Koksal, M., Kumar, P., Bolin, J.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.289 
• R-Value Work: 0.254 
• R-Value Observed: 0.256 

Literature

Crystal structure of a dibenzofuran-degrading dioxygenase: an unusual spatially heterogeneous crystal with a hypersymmetric intensity distribution

Koksal, M., Kumar, P., Fortin, P.D., Eltis, L.D., Bolin, J.T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 130.23 kDa 
• Atom Count: 9,162 
• Modelled Residue Count: 1,156 
• Deposited Residue Count: 1,176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase/bleomycin resistance protein/dioxygenase	A, B, C, D	294	Rhizorhabdus wittichii RW1	Mutation(s): 0  Gene Names: dbfB, Swit_4902 EC: 1.13.11

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	F [auth A], I [auth B]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
SO4	G [auth A], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FE2	E [auth A], H [auth B], K [auth C], L [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.289 
• R-Value Work: 0.254 
• R-Value Observed: 0.256 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.587	α = 90
b = 131.587	β = 90
c = 103.146	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Koksal, M., Kumar, P., Bolin, J.T.

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-04-03
  Changes: Refinement description