7YJ0

Structural basis of oxepinone formation by a flavin-monooxygenase VibO

• PDB DOI: https://doi.org/10.2210/pdb7YJ0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Boreostereum vibrans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-18 Released: 2023-05-10 
• Deposition Author(s): Zhang, M.F., Pan, L.F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.230 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

Literature

A flavin-monooxygenase catalyzing oxepinone formation and the complete biosynthesis of vibralactone

Feng, K.N., Zhang, Y., Zhang, M., Yang, Y.L., Liu, J.K., Pan, L., Zeng, Y.

(2023) Nat Commun 14: 3436

• DOI: https://doi.org/10.1038/s41467-023-39108-x

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: equilibrium centrifugation

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 290.49 kDa 
• Atom Count: 19,937 
• Modelled Residue Count: 2,480 
• Deposited Residue Count: 2,612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VibO	A, B, C, D	653	Boreostereum vibrans	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], I [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
GOL (Subject of Investigation/LOI)	H [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.230 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.083	α = 89.874
b = 92.504	β = 74.919
c = 104.639	γ = 75.746

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data scaling
PDB_EXTRACT	data extraction
autoPROC	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-10 
Deposition Author(s): Zhang, M.F., Pan, L.F.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21977101; 21822705

Revision History  

• Version 1.0: 2023-05-10
  Type: Initial release
  
• Version 1.1: 2023-05-17
  Changes: Derived calculations
• Version 1.2: 2023-06-21
  Changes: Database references