1HAN|pdb_00001han
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.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.190 (Depositor)
- R-Value Work: 0.162 (Depositor)
- R-Value Observed: 0.162 (Depositor)
wwPDB Validation 3D Report Full Report
Download MendeleyCrystal 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 Search on PubMed
- 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.
Explore in 3D: Structure |Sequence Annotations |Validation Report |Ligand Interaction (TBU)
Global Symmetry: Dihedral - D4 (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8
Find Similar Assemblies
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
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE | 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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P47228 | ||||
Sequence AnnotationsExpand | |||||
| |||||
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D 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
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.190 (Depositor)
- R-Value Work: 0.162 (Depositor)
- R-Value Observed: 0.162 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 122.58 | α = 90 |
| b = 122.58 | β = 90 |
| c = 111.36 | γ = 90 |
| Software Name | Purpose |
|---|---|
| X-PLOR | model building |
| X-PLOR | refinement |
| HKL | data reduction |
| X-PLOR | phasing |
Deposition Data
- Released Date: 1995-11-14 Deposition Author(s): Han, S.,Bolin, J.T.
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
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