8YB0

XFEL crystal structure of the reduced form of F393H P450BM3 with N-enanthyl-L-prolyl-L-phenylalanine in complex with styrene

• PDB DOI: https://doi.org/10.2210/pdb8YB0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Priestia megaterium NBRC 15308 = ATCC 14581
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-02-11 Released: 2025-02-12 
• Deposition Author(s): Nagao, S., Kuwano, W., Tosha, T., Yamashita, K., Stanfield, J.K., Kasai, C., Ariyasu, S., Shoji, O., Sugimoto, H., Kubo, M.
• Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.205 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

XFEL Crystallography Reveals Dynamic Control of Non-Natural Substrate Binding in Cytochrome P450BM3 Catalytic Cycle

Nagao, S., Kuwano, W., Tosha, T., Yamashita, K., Stanfield, J.K., Kasai, C., Ariyasu, S., Shoji, O., Sugimoto, H., Kubo, M.

To be published.

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 107.22 kDa 
• Atom Count: 8,450 
• Modelled Residue Count: 910 
• Deposited Residue Count: 910 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional cytochrome P450/NADPH--P450 reductase	A, B	455	Priestia megaterium NBRC 15308 = ATCC 14581	Mutation(s): 1  EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (PDB Primary Data)
UniProt
Find proteins for P14779 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19)) Explore P14779  Go to UniProtKB:  P14779

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	C [auth A], I [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
D0L	D [auth A], J [auth B]	(2S)-2-[[(2S)-1-heptylpyrrolidin-2-yl]carbonylamino]-3-phenyl-propanoic acid C21 H32 N2 O3 UZXMNGCHFSENBI-OALUTQOASA-N
SYN (Subject of Investigation/LOI)	E [auth A], K [auth B]	ethenylbenzene C8 H8 PPBRXRYQALVLMV-UHFFFAOYSA-N
GOL	F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.205 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.83	α = 90
b = 128.43	β = 90
c = 149.53	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Nagao, S., Kuwano, W., Tosha, T., Yamashita, K., Stanfield, J.K., Kasai, C., Ariyasu, S., Shoji, O., Sugimoto, H., Kubo, M.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJCR15P3
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H05784
Japan Society for the Promotion of Science (JSPS)	Japan	JP18KK0397
Japan Society for the Promotion of Science (JSPS)	Japan	JP19K22403

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release