8YB2

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

PDB DOI: https://doi.org/10.2210/pdb8YB2/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 ?
R-Value Free:
0.208 (Depositor), 0.208 (DCC)
R-Value Work:
0.179 (Depositor), 0.179 (DCC)
R-Value Observed:
0.181 (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

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.

Macromolecule Content

Total Structure Weight: 107.28 kDa
Atom Count: 8,356
Modelled Residue Count: 910
Deposited Residue Count: 910
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14779
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
D0L Query on D0L Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B]	D [auth A], K [auth B]	(2S)-2-[[(2S)-1-heptylpyrrolidin-2-yl]carbonylamino]-3-phenyl-propanoic acid C₂₁ H₃₂ N₂ O₃ UZXMNGCHFSENBI-OALUTQOASA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]
SYN (Subject of Investigation/LOI) Query on SYN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B]	E [auth A], L [auth B]	ethenylbenzene C₈ H₈ PPBRXRYQALVLMV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	G [auth A] H [auth A] I [auth A] N [auth B] O [auth B] G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
OXY (Subject of Investigation/LOI) Query on OXY Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B]	F [auth A], M [auth B]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 ?
R-Value Free: 0.208 (Depositor), 0.208 (DCC)
R-Value Work: 0.179 (Depositor), 0.179 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 58.83	α = 90
b = 128.51	β = 90
c = 149.42	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-02-12

Deposition Author(s):

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