3TH1

Crystal structure of chlorocatechol 1,2-dioxygenase from Pseudomonas putida

• PDB DOI: https://doi.org/10.2210/pdb3TH1/pdb

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


• Deposited: 2011-08-18 Released: 2012-08-22 
• Deposition Author(s): Rustiguel, J.K., Nonato, M.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.279 
• R-Value Work: 0.227 
• R-Value Observed: 0.232 

Literature

Crystal Structure of chlorocatechol 1,2-dioxygenase from Pseudomonas putida

Rustiguel, J.K., Barbosa, L.R.S., Araujo, A.P.U., Nonato, M.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 89.25 kDa 
• Atom Count: 5,462 
• Modelled Residue Count: 727 
• Deposited Residue Count: 780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorocatechol 1,2-dioxygenase	A, B, C	260	Pseudomonas putida	Mutation(s): 0  Gene Names: clcA EC: 1.13.11
UniProt
Find proteins for P11451 (Pseudomonas putida) Explore P11451  Go to UniProtKB:  P11451

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3PH	F [auth A], M [auth B]	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE C39 H77 O8 P YFWHNAWEOZTIPI-DIPNUNPCSA-N
DTD	E [auth A], L [auth B]	DITHIANE DIOL C4 H8 O2 S2 YPGMOWHXEQDBBV-IMJSIDKUSA-N
GOL	J [auth B], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE	D [auth A], K [auth B], O [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG	G [auth A], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.279 
• R-Value Work: 0.227 
• R-Value Observed: 0.232 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.57	α = 90
b = 97.57	β = 90
c = 423.6	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-22 
Deposition Author(s): Rustiguel, J.K., Nonato, M.C.

Revision History  

• Version 1.0: 2012-08-22
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Advisory, Refinement description
• Version 1.2: 2023-09-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description