9PFX | pdb_00009pfx

Crystal structure of native HDO-family N-oxygenase RohS from Pseudomonas brassicacearum strain DF41 (PbrRohS)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.218 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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Literature

Crystal structure of RohS, a heme-oxygenase-like N-oxygenase from azomycin biosynthesis.

Wei, Z.W.Salamon, P.Higgins, M.A.Ryan, K.S.

(2026) J Biological Chem 302: 111389-111389

  • DOI: https://doi.org/10.1016/j.jbc.2026.111389
  • Primary Citation Related Structures: 
    9PFW, 9PFX

  • PubMed Abstract: 

    The nitro group is an important functional group found in the nitroimidazoles, antibiotic therapeutics for anaerobic pathogens. In the biosynthetic pathway to the nitroimidazole antibiotic azomycin, a nitro-forming enzyme RohS - a member of the heme-oxygenase-like dimetal/domain-containing oxidase/oxygenase (HDO) family - catalyzes a six-electron oxidation of 2-aminoimidazole to 2-nitroimidazole. Here we present the 2.20 Å resolution crystal structure of RohS and identify a potential active site pocket consisting of seven key residues important for metal coordination. By comparing the structures and sequences of two RohS homologs - one functionally active and one inactive - we convert the inactive RohS to its active form, thus revealing a key residue for metal coordination in RohS catalysis. Altogether, our work provides structural basis for further mechanistic investigation of this six-electron oxidation process and provides insight into the expanding repertoire of the HDO protein family and nitro-formation N-oxygenases.


  • Organizational Affiliation
    • Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada.

Macromolecule Content 

  • Total Structure Weight: 35.15 kDa 
  • Atom Count: 2,459 
  • Modeled Residue Count: 289 
  • Deposited Residue Count: 306 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PbrRohS306Pseudomonas brassicacearumMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.218 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.857α = 90
b = 93.857β = 90
c = 43.286γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2021-02626

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-01
    Type: Initial release
  • Version 1.1: 2026-05-13
    Changes: Database references