9NK3 | pdb_00009nk3

Prenylated-FMN maturase PhdC E45A mutant from Mycolicibacterium fortuitum (apo)

• PDB DOI: https://doi.org/10.2210/pdb9NK3/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Mycolicibacterium fortuitum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-02-28 Released: 2026-02-18 
• Deposition Author(s): Kilde, I.R., Koutmos, M.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 
  0.146 (Depositor), 0.146 (DCC) 
• R-Value Work: 
  0.120 (Depositor), 0.120 (DCC) 

Starting Model: experimental

Literature

Structure and Mechanism of the Prenylated-FMN Maturase, PhdC

DiRocco, D.J., Kilde, I., Langford, D.P., Roy, P., Bhaumik, S., Mendoza, J., Koutmos, M., Marsh, E.N.G.

(2026) ACS Catal 16: 1773-1782

• DOI: https://doi.org/10.1021/acscatal.5c08793

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: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 18.98 kDa 
• Atom Count: 1,381 
• Modeled Residue Count: 154 
• Deposited Residue Count: 168 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxamine 5'-phosphate oxidase putative domain-containing protein	A	168	Mycolicibacterium fortuitum	Mutation(s): 1  Gene Names: XA26_16660
UniProt
Find proteins for A0A0N9XAG5 (Mycolicibacterium fortuitum) Explore A0A0N9XAG5  Go to UniProtKB:  A0A0N9XAG5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	D [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
EDO	C [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free:  0.146 (Depositor), 0.146 (DCC) 
• R-Value Work:  0.120 (Depositor), 0.120 (DCC) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.801	α = 90
b = 75.605	β = 90
c = 80.895	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
autoPROC	data reduction
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-02-18 
Deposition Author(s): Kilde, I.R., Koutmos, M.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE 2203729
National Science Foundation (NSF, United States)	United States	CHE 1904759

Revision History  

• Version 1.0: 2026-02-18
  Type: Initial release