› 8yay

X-ray diffraction
1.8Å resolution

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

Released:
DOI: 10.2210/pdb8yay/pdb
Model geometry
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PDB entry 8yay coloured by chain, front view.
PDB entry 8yay coloured by chain, side view.
PDB entry 8yay coloured by chain, top view.
Source organism: Priestia megaterium NBRC 15308 = ATCC 14581
Primary publication:
XFEL crystallography reveals catalytic cycle dynamics during non-native substrate oxidation by cytochrome P450BM3.
Nagao S, Kuwano W, Tosha T, Yamashita K, Stanfield JK, Kasai C, Ariyasu S, Hirata K, Ueno G, Murakami H, Ago H, Yamamoto M, Shoji O, Sugimoto H, Kubo M
Commun Chem 8 63 (2025)
PMID: 40075209

Function and Biology Details

Reactions catalysed: 
RH + [reduced NADPH--hemoprotein reductase] + O(2) = ROH + [oxidized NADPH--hemoprotein reductase] + H(2)O
NADPH + n oxidized hemoprotein = NADP(+) + n reduced hemoprotein
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-147081 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Bifunctional cytochrome P450/NADPH--P450 reductase Chains: A, B
Molecule details ›
Chains: A, B
Length: 455 amino acids
Theoretical weight: 52.16 KDa
Source organism: Priestia megaterium NBRC 15308 = ATCC 14581
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P14779 (Residues: 2-456; Coverage: 43%)
Gene names: BG04_163, cyp102, cyp102A1
Sequence domains: Cytochrome P450

Ligands and Environments


Cofactor: Ligand HEM 2 x HEM
3 bound ligands:
Ligand D0L 2 x D0L
Ligand SYN 2 x SYN
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SACLA BEAMLINE BL2
Spacegroup: P212121
Unit cell:
a: 58.91Å b: 128.64Å c: 149.45Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.172 0.211
Expression system: Escherichia coli BL21(DE3)

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