2GBX

Crystal Structure of Biphenyl 2,3-Dioxygenase from Sphingomonas yanoikuyae B1 Bound to Biphenyl

• PDB DOI: https://doi.org/10.2210/pdb2GBX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sphingobium yanoikuyae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-03-12 Released: 2007-03-20 
• Deposition Author(s): Ferraro, D.J., Brown, E.N., Yu, C., Parales, R.E., Gibson, D.T., Ramaswamy, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.268 
• R-Value Work: 0.237 
• R-Value Observed: 0.238 

Literature

Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1.

Ferraro, D.J., Brown, E.N., Yu, C.L., Parales, R.E., Gibson, D.T., Ramaswamy, S.

(2007) BMC Struct Biol 7: 10-10

• PubMed: 17349044 
• DOI: https://doi.org/10.1186/1472-6807-7-10
• Primary Citation of Related Structures:  
  2GBW, 2GBX, 2I7F


• PubMed Abstract: 
  

  The initial step involved in oxidative hydroxylation of monoaromatic and polyaromatic compounds by the microorganism Sphingobium yanoikuyae strain B1 (B1), previously known as Sphingomonas yanoikuyae strain B1 and Beijerinckia sp. strain B1, is performed by a set of multiple terminal Rieske non-heme iron oxygenases. These enzymes share a single electron donor system consisting of a reductase and a ferredoxin (BPDO-FB1). One of the terminal Rieske oxygenases, biphenyl 2,3-dioxygenase (BPDO-OB1), is responsible for B1's ability to dihydroxylate large aromatic compounds, such as chrysene and benzo[a]pyrene.

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Organizational Affiliation: 

Department of Biochemistry, University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, Iowa, 52242, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

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

Macromolecule Content

• Total Structure Weight: 217.22 kDa 
• Atom Count: 15,278 
• Modelled Residue Count: 1,854 
• Deposited Residue Count: 1,884 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Biphenyl 2,3-Dioxygenase Alpha Subunit	A, C, E	454	Sphingobium yanoikuyae	Mutation(s): 0  Gene Names: bphA1fA2f
UniProt
Find proteins for A2TC87 (Sphingobium yanoikuyae) Explore A2TC87  Go to UniProtKB:  A2TC87

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Biphenyl 2,3-Dioxygenase Beta Subunit	B, D, F	174	Sphingobium yanoikuyae	Mutation(s): 0
UniProt
Find proteins for A2TC88 (Sphingobium yanoikuyae) Explore A2TC88  Go to UniProtKB:  A2TC88

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES	H [auth A], N [auth C], T [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
BNL	I [auth A], O [auth C], U [auth E]	BIPHENYL C12 H10 ZUOUZKKEUPVFJK-UHFFFAOYSA-N
ZN	J [auth B], K [auth B], L [auth B], P [auth D], Q [auth D], R [auth D], V [auth F], W [auth F], X [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE	G [auth A], M [auth C], S [auth E]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.268 
• R-Value Work: 0.237 
• R-Value Observed: 0.238 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.94	α = 90
b = 133.94	β = 90
c = 219.708	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-20 
Deposition Author(s): Ferraro, D.J., Brown, E.N., Yu, C., Parales, R.E., Gibson, D.T., Ramaswamy, S.

Revision History  

• Version 1.0: 2007-03-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description