2CKF | pdb_00002ckf

Crystal Structure of the Terminal Component of the PAH-hydroxylating Dioxygenase from Sphingomonas sp CHY-1

• PDB DOI: https://doi.org/10.2210/pdb2CKF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sphingomonas sp. CHY-1
• Expression System: Pseudomonas putida
• Mutation(s): No 


• Deposited: 2006-04-18 Released: 2007-01-02 
• Deposition Author(s): Jakoncic, J., Meyer, C., Jouanneau, Y., Stojanoff, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: other

Literature

The Catalytic Pocket of the Ring-Hydroxylating Dioxygenase from Sphingomonas Chy-1.

Jakoncic, J., Jouanneau, Y., Meyer, C., Stojanoff, V.

(2007) Biochem Biophys Res Commun 352: 861

• PubMed: 17157819 
• DOI: https://doi.org/10.1016/j.bbrc.2006.11.117
• Primary Citation Related Structures: 
  2CKF


• PubMed Abstract: 
  

  Ring-hydroxylating dioxygenases are multicomponent bacterial enzymes that catalyze the first step in the oxidative degradation of aromatic hydrocarbons. The dioxygenase from Sphingomonas CHY-1 is unique in that it can oxidize a wide range of polycyclic aromatic hydrocarbons (PAHs). With a crystal structure similar to that of the seven other known dioxygenases, its catalytic domain features the largest hydrophobic substrate binding cavity characterized so far. Molecular modeling studies indicated that the catalytic cavity is large enough to accommodate a five-ring benzo[a]pyrene molecule. The predicted positions of this and other PAHs in the substrate binding pocket are consistent with the product regio- and stereo-selectivity of the enzyme.

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Organizational Affiliation: 
• Brookhaven National Laboratory, National Synchrotron Light Source, Upton, NY 11973, USA.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 215.74 kDa 
• Atom Count: 15,833 
• Modeled Residue Count: 1,816 
• Deposited Residue Count: 1,884 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RING-HYDROXYLATING DIOXYGENASE ALPHA SUBUNIT	A, C, E	454	Sphingomonas sp. CHY-1	Mutation(s): 0
UniProt
Find proteins for Q65AT1 (Sphingomonas sp. CHY-1) Explore Q65AT1  Go to UniProtKB:  Q65AT1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RING-HYDROXYLATING DIOXYGENASE BETA SUBUNIT	B, D, F	174	Sphingomonas sp. CHY-1	Mutation(s): 0
UniProt
Find proteins for Q65AT0 (Sphingomonas sp. CHY-1) Explore Q65AT0  Go to UniProtKB:  Q65AT0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES	G [auth A], I [auth C], K [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
FE	H [auth A], J [auth C], L [auth E]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.644	α = 90
b = 112.73	β = 90
c = 190.626	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-02 
Deposition Author(s): Jakoncic, J., Meyer, C., Jouanneau, Y., Stojanoff, V.

Revision History  

• Version 1.0: 2007-01-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description