8VOT | pdb_00008vot

The crystal structure of wild-type CYP199A4 bound to 4-(hydroxymethyl)benzoic acid

• PDB DOI: https://doi.org/10.2210/pdb8VOT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodopseudomonas palustris HaA2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-01-16 Released: 2025-08-13 
• Deposition Author(s): Podgorski, M.N., Bell, S.G.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.168 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.137 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Starting Model: experimental

Literature

Investigating the Correlation between Product Release and Solvation in Cytochrome P450 Enzymes

Podgorski, M.N., Martinez-Castro, L., Bruning, J.B., Campbell, E.C., Marechal, J.D., Bell, S.G.

(2025) ACS Catal 15: 2867-2884

• DOI: https://doi.org/10.1021/acscatal.4c05873

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 45.44 kDa 
• Atom Count: 3,788 
• Modeled Residue Count: 393 
• Deposited Residue Count: 410 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A	410	Rhodopseudomonas palustris HaA2	Mutation(s): 0  Gene Names: RPB_3613
UniProt
Find proteins for Q2IU02 (Rhodopseudomonas palustris (strain HaA2)) Explore Q2IU02  Go to UniProtKB:  Q2IU02

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
E5X (Subject of Investigation/LOI)	B [auth A]	4-(hydroxymethyl)benzoic acid C8 H8 O3 WWYFPDXEIFBNKE-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.168 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.137 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.227	α = 90
b = 51.405	β = 91.91
c = 79.502	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Podgorski, M.N., Bell, S.G.

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

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release
  
• Version 1.1: 2025-08-20
  Changes: Database references