2BUZ

Crystal Structure of Protocatechuate 3,4-Dioxygenase from Acinetobacter Sp. ADP1 Mutant R133H in Complex with 4-Nitrocatechol

• PDB DOI: https://doi.org/10.2210/pdb2BUZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acinetobacter baylyi ADP1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-06-20 Released: 2006-11-01 
• Deposition Author(s): Vetting, M.W., Valley, M.P., D'Argenio, D.A., Ornston, L.N., Lipscomb, J.D., Ohlendorf, D.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.202 
• R-Value Work: 0.173 
• R-Value Observed: 0.173 

Starting Model: experimental

Literature

Crystallographic Studies of Intradiol Dioxygenases

Vetting, M.W.

(2001) Ph D Thesis 

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Hetero 24-mer - A12B12 Pseudo Symmetry: Tetrahedral - T  (Explore in 3D)
Pseudo Stoichiometry: Homo 24-mer - A24 

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

Macromolecule Content

• Total Structure Weight: 51.28 kDa 
• Atom Count: 3,760 
• Modelled Residue Count: 440 
• Deposited Residue Count: 450 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN	A	209	Acinetobacter baylyi ADP1	Mutation(s): 1  EC: 1.13.11.3
UniProt
Find proteins for P20371 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore P20371  Go to UniProtKB:  P20371

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN	B	241	Acinetobacter baylyi ADP1	Mutation(s): 0  EC: 1.13.11.3
UniProt
Find proteins for P20372 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore P20372  Go to UniProtKB:  P20372

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4NC	D [auth B]	4-NITROCATECHOL C6 H5 N O4 XJNPNXSISMKQEX-UHFFFAOYSA-N
FE	C [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.202 
• R-Value Work: 0.173 
• R-Value Observed: 0.173 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.09	α = 90
b = 145.09	β = 90
c = 145.09	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-01 
Deposition Author(s): Vetting, M.W., Valley, M.P., D'Argenio, D.A., Ornston, L.N., Lipscomb, J.D., Ohlendorf, D.H.

Revision History  

• Version 1.0: 2006-11-01
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-06-20
  Changes: Data collection, Structure summary
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description