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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.254 (Depositor), 0.254 (DCC)
R-Value Work:
0.218 (Depositor), 0.223 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20586
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
A1LXW (Subject of Investigation/LOI) Query on A1LXW Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	3-methyl-4-oxidanyl-benzoic acid C₈ H₈ O₃ LTFHNKUKQYVHDX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.254 (Depositor), 0.254 (DCC)
R-Value Work: 0.218 (Depositor), 0.223 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.