1DLM

STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER CALCOACETICUS NATIVE DATA

• PDB DOI: https://doi.org/10.2210/pdb1DLM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acinetobacter baylyi ADP1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-12-11 Released: 2000-05-23 
• Deposition Author(s): Vetting, M.W., Ohlendorf, D.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.243 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

Literature

The 1.8 A crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker.

Vetting, M.W., Ohlendorf, D.H.

(2000) Structure 8: 429-440

• PubMed: 10801478 
• DOI: https://doi.org/10.1016/s0969-2126(00)00122-2


• PubMed Abstract: 
  

  Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. Catechol 1,2-dioxygenases (1, 2-CTDs) have a rudimentary design structure - a homodimer with one catalytic non-heme ferric ion per monomer, that is (alphaFe(3+))(2). This is in contrast to the archetypical intradiol dioxygenase protocatechuate 3,4-dioxygenase (3,4-PCD), which forms more diverse oligomers, such as (alphabetaFe(3+))(2-12).

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Organizational Affiliation: 

The department of Biochemistry, Molecular Biology and Biophysics, Center for Metals in Biocatalysis, University of Minnesota Medical School, Minneapolis, MN 55455-0347, USA.

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)

Macromolecule Content

• Total Structure Weight: 70.15 kDa 
• Atom Count: 5,085 
• Modelled Residue Count: 618 
• Deposited Residue Count: 622 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATECHOL 1,2-DIOXYGENASE	A, B	311	Acinetobacter baylyi ADP1	Mutation(s): 0  EC: 1.13.11.1
UniProt
Find proteins for P07773 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore P07773  Go to UniProtKB:  P07773

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LIO	D [auth A], F [auth B]	[1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL CHOLINE C33 H67 N O8 P YAOVLDDMIGILIT-WJOKGBTCSA-O
FE	C [auth A], E [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.243 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.6	α = 90
b = 87.6	β = 96.3
c = 84.2	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
X-GEN	data reduction
X-GEN	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-05-23 
Deposition Author(s): Vetting, M.W., Ohlendorf, D.H.

Revision History  

• Version 1.0: 2000-05-23
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations