1HAN

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

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 

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This is version 1.3 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

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


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE297Paraburkholderia xenovorans LB400Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47228
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TBU
Query on TBU
Download Ideal Coordinates CCD File 
D [auth A]TERTIARY-BUTYL ALCOHOL
C4 H10 O
DKGAVHZHDRPRBM-UHFFFAOYSA-N
FE
Query on FE
Download Ideal Coordinates CCD File 
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 = 122.58α = 90
b = 122.58β = 90
c = 111.36γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
HKLdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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