8IHG | pdb_00008ihg

Crystal structure of aminophenol dioxygenase from Pseudomonas species AP-3

• PDB DOI: https://doi.org/10.2210/pdb8IHG/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Pseudomonas sp.
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-02-22 Released: 2024-02-28 
• Deposition Author(s): Shi, Q.L., Su, D.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 
  0.234 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of aminophenol dioxygenase from Pseudomonas species AP-3

Shi, Q.L., Su, D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 128.42 kDa 
• Atom Count: 9,034 
• Modeled Residue Count: 1,139 
• Deposited Residue Count: 1,154 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-aminophenol 1,6-dioxygenase beta subunit	A, C	305	Pseudomonas sp.	Mutation(s): 0  Gene Names: amnB EC: 1.13.11.74
UniProt
Find proteins for O33477 (Pseudomonas sp) Explore O33477  Go to UniProtKB:  O33477

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
2-aminophenol 1,6-dioxygenase alpha subunit	B, D	272	Pseudomonas sp.	Mutation(s): 0  Gene Names: amnA
UniProt
Find proteins for O33478 (Pseudomonas sp) Explore O33478  Go to UniProtKB:  O33478

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2AF (Subject of Investigation/LOI)	F [auth A], G [auth C]	2-AMINOPHENOL C6 H7 N O CDAWCLOXVUBKRW-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)	H [auth C], J [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	E [auth A], I [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free:  0.234 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.475	α = 90
b = 153.475	β = 90
c = 312.036	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-28 
Deposition Author(s): Shi, Q.L., Su, D.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2017YFA0505903

Revision History  

• Version 1.0: 2024-02-28
  Type: Initial release