PDB-9nk0: Prenylated-FMN maturase PhdC from Mycolicibacterium fortuitum (apo)

ID or keywords:

Entry

Database: PDB / ID: 9nk0

Title

Prenylated-FMN maturase PhdC from Mycolicibacterium fortuitum (apo)

Components

Pyridoxamine 5'-phosphate oxidase putative domain-containing protein

Keywords

FLAVOPROTEIN / Maturase / homodimer / beta-sandwhich

Function / homology

Pyridoxamine 5'-phosphate oxidase putative domain-containing protein

Function and homology information

Biological species

Mycolicibacterium fortuitum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.52 Å

Authors

Kilde, I.R. / Koutmos, M.

Funding support

United States, 2items

Citation

Journal: Acs Catalysis / Year: 2026
Title: Structure and Mechanism of the Prenylated-FMN Maturase, PhdC
Authors: DiRocco, D.J. / Kilde, I. / Langford, D.P. / Roy, P. / Bhaumik, S. / Mendoza, J. / Koutmos, M. / Marsh, E.N.G.

History

Deposition	Feb 28, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 18, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9nk0.cif.gz	174.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9nk0.ent.gz	111 KB	Display	PDB format
PDBx/mmJSON format	9nk0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nk/9nk0 ftp://data.pdbj.org/pub/pdb/validation_reports/nk/9nk0	HTTPS FTP

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Related structure data

Related structure data	9nk1C 9nk2C 9nk3C 9nk4C 9o5mC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Pyridoxamine 5'-phosphate oxidase putative domain-containing protein

hetero molecules

18.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: mass spectrometry

Unit cell

Length a, b, c (Å)	60.083, 76.697, 80.594
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	23
Space group name H-M	I222

#1: Protein	Pyridoxamine 5'-phosphate oxidase putative domain-containing protein Mass: 18708.115 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium fortuitum (bacteria) / Strain: CT6 / Gene: XA26_16660 / Plasmid: pCDFduet-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N9XAG5
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.43 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2:1 protein (20mM bistris pH 7.2, 200mM KCl, 1mM MnCl2, 5% glycerol) to condition (30% w/v PEG 5000 MME, 100 mM MES/ Sodium hydroxide pH 6.5, 200 mM ammonium sulfate)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.987 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2024
Radiation	Monochromator: Liquid Nireogen Doubke / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 1.52→38.35 Å / Num. obs: 28916 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC_1/2: 1 / R_merge(I) obs: 0.025 / R_rim(I) all: 0.027 / Net I/σ(I): 46
Reflection shell	Resolution: 1.52→1.55 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.98 / Mean I/σ(I) obs: 16.9 / Num. unique obs: 9655 / CC_1/2: 0.995 / R_pim(I) all: 0.57 / R_rim(I) all: 0.106 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.88)	refinement
autoPROC		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.52→38.348 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.963 / SU B: 2.005 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.058
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1648	1502	5.194 %
R_work	0.1267	27414	-
all	0.129	-	-
obs	-	28916	99.539 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 19.046 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.107 Å²	0 Å²	-0 Å²
2-	-	0.22 Å²	0 Å²
3-	-	-	1.887 Å²

Refinement step

Cycle: LAST / Resolution: 1.52→38.348 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1198	0	13	163	1374

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	1285
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	1248
X-RAY DIFFRACTION	r_angle_refined_deg	1.977	1.855	1740
X-RAY DIFFRACTION	r_angle_other_deg	0.805	1.775	2864
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.911	5	165
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	14.155	5	18
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.838	10	220
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.662	10	60
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	195
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	1568
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	310
X-RAY DIFFRACTION	r_nbd_refined	0.247	0.2	209
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.163	0.2	1055
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	613
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	703
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.174	0.2	111
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.039	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.073	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.189	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.123	0.2	75
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.213	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	5.513	1.549	637
X-RAY DIFFRACTION	r_mcbond_other	5.513	1.552	638
X-RAY DIFFRACTION	r_mcangle_it	7.88	2.797	800
X-RAY DIFFRACTION	r_mcangle_other	7.887	2.8	801
X-RAY DIFFRACTION	r_scbond_it	8.396	1.985	648
X-RAY DIFFRACTION	r_scbond_other	8.392	1.986	649
X-RAY DIFFRACTION	r_scangle_it	11.826	3.449	937
X-RAY DIFFRACTION	r_scangle_other	11.82	3.449	938
X-RAY DIFFRACTION	r_lrange_it	18.394	18.074	1401
X-RAY DIFFRACTION	r_lrange_other	15.906	16.544	1353
X-RAY DIFFRACTION	r_rigid_bond_restr	5.272	3	2533

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.52-1.559	0.179	118	0.108	1996	0.112	2124	0.982	0.994	99.5292	0.103
1.559-1.602	0.149	92	0.096	1957	0.098	2051	0.988	0.996	99.9025	0.091
1.602-1.648	0.161	126	0.094	1894	0.098	2026	0.987	0.996	99.7038	0.091
1.648-1.699	0.142	90	0.097	1862	0.099	1959	0.991	0.996	99.6427	0.095
1.699-1.755	0.159	112	0.101	1774	0.105	1890	0.989	0.995	99.7884	0.1
1.755-1.816	0.174	99	0.103	1720	0.107	1822	0.983	0.995	99.8354	0.102
1.816-1.885	0.114	89	0.1	1679	0.101	1772	0.99	0.995	99.7743	0.099
1.885-1.961	0.166	90	0.109	1607	0.112	1709	0.98	0.993	99.2978	0.109
1.961-2.048	0.153	89	0.123	1539	0.124	1644	0.987	0.992	99.0268	0.126
2.048-2.148	0.168	79	0.122	1447	0.125	1550	0.983	0.992	98.4516	0.127
2.148-2.264	0.144	69	0.122	1452	0.123	1524	0.987	0.992	99.8031	0.128
2.264-2.401	0.175	52	0.119	1348	0.121	1402	0.983	0.991	99.8573	0.126
2.401-2.566	0.154	66	0.119	1273	0.121	1342	0.987	0.992	99.7765	0.13
2.566-2.77	0.172	67	0.126	1191	0.129	1259	0.985	0.99	99.9206	0.143
2.77-3.033	0.161	66	0.137	1088	0.138	1156	0.982	0.989	99.827	0.157
3.033-3.388	0.137	51	0.139	993	0.139	1046	0.989	0.988	99.8088	0.161
3.388-3.907	0.163	46	0.146	870	0.147	936	0.982	0.988	97.8632	0.175
3.907-4.773	0.146	42	0.126	761	0.127	805	0.989	0.991	99.7515	0.165
4.773-6.698	0.237	39	0.18	596	0.183	635	0.98	0.986	100	0.222
6.698-38.348	0.289	20	0.209	367	0.212	394	0.974	0.971	98.2234	0.27

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