9JS9 | pdb_00009js9

Crystal structure of the CYP154C5 F92A/R114A/T248G/E282A variant from Nocardia farcinica

PDB DOI: https://doi.org/10.2210/pdb9JS9/pdb

Classification: OXIDOREDUCTASE
Organism(s): Nocardia farcinica IFM 10152
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-09-30 Released: 2025-10-22
Deposition Author(s): Qin, M.M., Fan, S.X., Cong, Z.Q., Jiang, Y.P.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.243 (Depositor), 0.243 (DCC)
R-Value Work:
0.203 (Depositor), 0.203 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Semirationally Engineering an Efficient P450 Peroxygenase for Regio- and Enantioselective Hydroxylation of Steroids

Fan, S., Qin, M., Wang, Q., Jiang, Y., Cong, Z.

(2025) ACS Catal 15: 2977-2986

DOI: https://doi.org/10.1021/acscatal.4c06342

Macromolecule Content

Total Structure Weight: 48.03 kDa
Atom Count: 3,471
Modeled Residue Count: 399
Deposited Residue Count: 429
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 monooxygenase	A [auth B]	429	Nocardia farcinica IFM 10152	Mutation(s): 4 Gene Names: NFA_53110
UniProt
Find proteins for Q5YNS8 (Nocardia farcinica (strain IFM 10152)) Explore Q5YNS8 Go to UniProtKB: Q5YNS8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5YNS8
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 MOL2 format, chain B mmCIF format, chain B	B	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B Interactions & Density Focus chain B
TES (Subject of Investigation/LOI) Query on TES Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	TESTOSTERONE C₁₉ H₂₈ O₂ MUMGGOZAMZWBJJ-DYKIIFRCSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.243 (Depositor), 0.243 (DCC)
R-Value Work: 0.203 (Depositor), 0.203 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.648	α = 90
b = 61.679	β = 113.95
c = 68.164	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
autoPROC	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-10-22
Type: Initial release
Version 1.1: 2025-11-05
Changes: Database references

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.