8Y2S | pdb_00008y2s

P-hydroxybenzoate hydroxylase complexed with 4-hydroxy-3-methylbenzoic acid

• PDB DOI: https://doi.org/10.2210/pdb8Y2S/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-01-27 Released: 2024-05-01 
• Deposition Author(s): Hara, K., Hashimoto, H., Matsushita, T., Kishimoto, S., Watanabe, K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Functional Enhancement of Flavin-Containing Monooxygenase through Machine Learning Methodology

Matsushita, T., Kishimoto, S., Hara, K., Hashimoto, H., Yamaguchi, H., Saito, Y., Watanabe, K.

(2024) ACS Catal 14: 6945-6951

• DOI: https://doi.org/10.1021/acscatal.4c00826

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.21 kDa 
• Atom Count: 3,244 
• Modeled Residue Count: 391 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxybenzoate 3-monooxygenase	A	400	Pseudomonas aeruginosa	Mutation(s): 2  Gene Names: pobA, CGU42_30330, GNQ48_09340, IPC737_09120 EC: 1.14.13.2
UniProt
Find proteins for P20586 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P20586  Go to UniProtKB:  P20586

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	C [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
A1LXW (Subject of Investigation/LOI)	B [auth A]	3-methyl-4-oxidanyl-benzoic acid C8 H8 O3 LTFHNKUKQYVHDX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.251	α = 90
b = 141.9	β = 90
c = 89.571	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-01 
Deposition Author(s): Hara, K., Hashimoto, H., Matsushita, T., Kishimoto, S., Watanabe, K.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-05-01
  Type: Initial release