9DY5 | pdb_00009dy5

The crystal structure of F182A CYP199A4 bound to 4-methylthiobenzoic acid

PDB DOI: https://doi.org/10.2210/pdb9DY5/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhodopseudomonas palustris HaA2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-10-13 Released: 2025-08-20
Deposition Author(s): Podgorski, M.N., Bell, S.G.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.281 (Depositor), 0.280 (DCC)
R-Value Work:
0.237 (Depositor), 0.238 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Comparing and Combining Alternative Strategies for Enhancing Cytochrome P450 Peroxygenase Activity

Podgorski, M.N., Bell, S.G.

(2025) ACS Catal 15: 5191-5210

DOI: https://doi.org/10.1021/acscatal.4c07486

Macromolecule Content

Total Structure Weight: 45.3 kDa
Atom Count: 3,155
Modeled Residue Count: 393
Deposited Residue Count: 410
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A	410	Rhodopseudomonas palustris HaA2	Mutation(s): 1 Gene Names: RPB_3613
UniProt
Find proteins for Q2IU02 (Rhodopseudomonas palustris (strain HaA2)) Explore Q2IU02 Go to UniProtKB: Q2IU02
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2IU02
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM 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]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
4MI (Subject of Investigation/LOI) Query on 4MI 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]	4-methylsulfanylbenzoic acid C₈ H₈ O₂ S KWHCPERWLHBLOT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.281 (Depositor), 0.280 (DCC)
R-Value Work: 0.237 (Depositor), 0.238 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.153	α = 90
b = 51.237	β = 93.47
c = 78.412	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-08-20

Deposition Author(s):

Podgorski, M.N.

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	--

Revision History (Full details and data files)

Version 1.0: 2025-08-20
Type: Initial release

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.