1HAN

CRYSTAL STRUCTURE OF THE BIPHENYL-CLEAVING EXTRADIOL DIOXYGENASE FROM A PCB-DEGRADING PSEUDOMONAD

• PDB DOI: https://doi.org/10.2210/pdb1HAN/pdb

• Classification: OXIDOREDUCTASE (OXYGENASE)
• Organism(s): Paraburkholderia xenovorans LB400
• Expression System: Burkholderia cepacia
• Mutation(s): No 


• Deposited: 1995-08-30 Released: 1995-11-14 
• Deposition Author(s): Han, S., Bolin, J.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.190 
• R-Value Work: 0.162 
• R-Value Observed: 0.162 

Literature

Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonad.

Han, S., Eltis, L.D., Timmis, K.N., Muchmore, S.W., Bolin, J.T.

(1995) Science 270: 976-980

• PubMed: 7481800 
• DOI: https://doi.org/10.1126/science.270.5238.976
• Primary Citation of Related Structures:  
  1HAN


• PubMed Abstract: 
  

  Polychlorinated biphenyls (PCBs) typify a class of stable aromatic pollutants that are targeted by bioremediation strategies. In the aerobic degradation of biphenyl by bacteria, the key step of ring cleavage is catalyzed by an Fe(II)-dependent extradiol dioxygenase. The crystal structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase from a PCB-degrading strain of Pseudomonas cepacia has been determined at 1.9 angstrom resolution. The monomer comprises amino- and carboxyl-terminal domains. Structural homology between and within the domains reveals evolutionary relationships within the extradiol dioxygenase family. The iron atom has five ligands in square pyramidal geometry: one glutamate and two histidine side chains, and two water molecules.

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Organizational Affiliation: 

Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content

• Total Structure Weight: 32.56 kDa 
• Atom Count: 2,352 
• Modelled Residue Count: 288 
• Deposited Residue Count: 297 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE	A	297	Paraburkholderia xenovorans LB400	Mutation(s): 0  Gene Names: BPHC EC: 1.13.11.39
UniProt
Find proteins for P47228 (Paraburkholderia xenovorans (strain LB400)) Explore P47228  Go to UniProtKB:  P47228

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TBU	D [auth A]	TERTIARY-BUTYL ALCOHOL C4 H10 O DKGAVHZHDRPRBM-UHFFFAOYSA-N
FE	B [auth A], C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.190 
• R-Value Work: 0.162 
• R-Value Observed: 0.162 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.58	α = 90
b = 122.58	β = 90
c = 111.36	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
HKL	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-11-14 
Deposition Author(s): Han, S., Bolin, J.T.

Revision History  

• Version 1.0: 1995-11-14
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other