8SM9 | pdb_00008sm9

Air-oxidized C. fi TruffO expressed from M9 minimal medium supplemented with Fe

• PDB DOI: https://doi.org/10.2210/pdb8SM9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cytobacillus firmus DS1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-04-25 Released: 2024-03-13 
• Deposition Author(s): Liu, C., Rittle, J.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Bioinformatic Discovery of a Cambialistic Monooxygenase.

Liu, C., Powell, M.M., Rao, G., Britt, R.D., Rittle, J.

(2024) J Am Chem Soc 146: 1783-1788

• PubMed: 38198693 
• DOI: https://doi.org/10.1021/jacs.3c12131
• Primary Citation Related Structures: 
  8SM6, 8SM7, 8SM8, 8SM9, 8SMA


• PubMed Abstract: 
  

  Dinuclear monooxygenases mediate challenging C-H bond oxidation reactions throughout nature. Many of these enzymes are presumed to exclusively utilize diiron cofactors. Herein we report the bioinformatic discovery of an orphan dinuclear monooxygenase that preferentially utilizes a heterobimetallic manganese-iron (Mn/Fe) cofactor to mediate an O ₂ -dependent C-H bond hydroxylation reaction. Unlike the structurally similar Mn/Fe-dependent monooxygenase AibH2, the diiron form of this enzyme (SfbO) exhibits a nascent enzymatic activity. This behavior raises the possibility that many other dinuclear monooxygenases may be endowed with the capacity to harness cofactors with a variable metal content.

---

Organizational Affiliation: 
• Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.
Department of Chemistry, University of California, Davis, Davis, California 95616, United States.

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 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: 167.63 kDa 
• Atom Count: 11,527 
• Modeled Residue Count: 1,376 
• Deposited Residue Count: 1,444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidohydrolase 2	A [auth F], B, C [auth D], D [auth H]	361	Cytobacillus firmus DS1	Mutation(s): 0  Gene Names: PBF_16344
UniProt
Find proteins for W7L2Y2 (Cytobacillus firmus DS1) Explore W7L2Y2  Go to UniProtKB:  W7L2Y2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE (Subject of Investigation/LOI)	E [auth F], F, G [auth B], H [auth B], I [auth D], J [auth D], K [auth H], L [auth H]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.818	α = 90
b = 67.88	β = 111.74
c = 138.508	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-03-13 
Deposition Author(s): Liu, C., Rittle, J.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-03-13
  Type: Initial release