PDB-9nk4: Prenylated-FMN maturase PhdC E45A mutant from Mycolicibacterium f...

ID or keywords:

Entry

Database: PDB / ID: 9nk4

Title

Prenylated-FMN maturase PhdC E45A mutant from Mycolicibacterium fortuitum bound to flavin mononucleotide

Components

Pyridoxamine 5'-phosphate oxidase putative domain-containing protein

Keywords

FLAVOPROTEIN / Maturase / homodimer / beta-sandwhich / prFMN

Function / homology

FLAVIN MONONUCLEOTIDE / 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: 1.27 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	9nk4.cif.gz	177.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9nk4.ent.gz	113.5 KB	Display	PDB format
PDBx/mmJSON format	9nk4.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/9nk4 ftp://data.pdbj.org/pub/pdb/validation_reports/nk/9nk4	HTTPS FTP

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Related structure data

Related structure data	9nk0C 9nk1C 9nk2C 9nk3C 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

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

1

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

hetero molecules

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

hetero molecules

defined by author&software
Evidence: mass spectrometry
38.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.003, 76.007, 80.115
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: 18650.078 Da / Num. of mol.: 1 / Mutation: E45A 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) / Strain (production host): DE3 / References: UniProt: A0A0N9XAG5
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.45 Å³/Da / Density % sol: 49.77 % / Description: Plates
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1:1 crystallization condition (0.2M ammonium acetate, 0.1M HEPES/NaOH pH 7.5, 45% v/v MPD) to buffer (20 mM BisTris pH 7.2 200 mM) PH range: 7.2-7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.689 Å
Detector	Type: DECTRIS EIGER2 XE CdTe 16M / Detector: PIXEL / Date: Oct 25, 2024
Radiation	Monochromator: At 26 m, Si (111), double crystal monochromator, horizontally deflecting, LN2 side-cooling Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.689 Å / Relative weight: 1
Reflection	Resolution: 1.27→30.52 Å / Num. obs: 47805 / % possible obs: 98.3 % / Redundancy: 10.3 % / CC_1/2: 0.998 / R_merge(I) obs: 0.082 / R_pim(I) all: 0.026 / R_rim(I) all: 0.086 / Χ²: 0.82 / Net I/σ(I): 15
Reflection shell	Resolution: 1.27→1.29 Å / R_merge(I) obs: 0.828 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2010 / CC_1/2: 0.516 / R_pim(I) all: 0.423 / R_rim(I) all: 0.94 / Χ²: 0.52 / % possible all: 84.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.100)	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.27→30.512 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.973 / SU B: 1.177 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.035
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1492	1829	3.826 %
R_work	0.1285	45973	-
all	0.129	-	-
obs	-	47802	98.332 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 19.346 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.138 Å²	-0 Å²	0 Å²
2-	-	0.378 Å²	-0 Å²
3-	-	-	0.76 Å²

Refinement step

Cycle: LAST / Resolution: 1.27→30.512 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1179	0	36	176	1391

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.012	1335
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	1257
X-RAY DIFFRACTION	r_angle_refined_deg	1.972	1.838	1824
X-RAY DIFFRACTION	r_angle_other_deg	0.888	1.768	2882
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.723	5	170
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.953	5	17
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.747	10	216
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.599	10	60
X-RAY DIFFRACTION	r_chiral_restr	0.113	0.2	206
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	1643
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	319
X-RAY DIFFRACTION	r_nbd_refined	0.258	0.2	231
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.174	0.2	1106
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	624
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	713
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.178	0.2	110
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.267	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.168	0.2	88
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.244	0.2	46
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.351	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	5.229	1.634	662
X-RAY DIFFRACTION	r_mcbond_other	5.226	1.638	663
X-RAY DIFFRACTION	r_mcangle_it	7.052	2.94	838
X-RAY DIFFRACTION	r_mcangle_other	7.062	2.944	839
X-RAY DIFFRACTION	r_scbond_it	8.391	1.966	673
X-RAY DIFFRACTION	r_scbond_other	8.406	1.968	670
X-RAY DIFFRACTION	r_scangle_it	11.348	3.458	986
X-RAY DIFFRACTION	r_scangle_other	11.342	3.456	987
X-RAY DIFFRACTION	r_lrange_it	17.576	22.218	1530
X-RAY DIFFRACTION	r_lrange_other	16.774	19.89	1483
X-RAY DIFFRACTION	r_rigid_bond_restr	4.49	3	2592

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
1.27-1.303	0.21	123	0.206	2939	0.206	3552	0.961	0.963	86.2049	0.167
1.303-1.339	0.195	126	0.175	3105	0.176	3483	0.975	0.976	92.7649	0.144
1.339-1.377	0.168	121	0.156	3135	0.156	3314	0.983	0.983	98.2498	0.129
1.377-1.42	0.143	121	0.139	3150	0.139	3273	0.987	0.987	99.9389	0.12
1.42-1.466	0.152	134	0.124	3074	0.125	3208	0.984	0.99	100	0.103
1.466-1.517	0.118	80	0.101	2971	0.102	3051	0.992	0.993	100	0.087
1.517-1.575	0.142	114	0.094	2865	0.096	2979	0.988	0.995	100	0.082
1.575-1.639	0.115	104	0.089	2742	0.09	2846	0.991	0.995	100	0.079
1.639-1.711	0.123	116	0.085	2621	0.086	2737	0.991	0.996	100	0.077
1.711-1.794	0.122	104	0.082	2550	0.084	2654	0.992	0.996	100	0.077
1.794-1.891	0.112	83	0.09	2410	0.091	2493	0.993	0.995	100	0.085
1.891-2.005	0.117	107	0.098	2276	0.099	2383	0.99	0.994	100	0.096
2.005-2.143	0.135	84	0.104	2149	0.105	2233	0.988	0.993	100	0.103
2.143-2.314	0.13	90	0.109	2015	0.11	2105	0.991	0.993	100	0.111
2.314-2.533	0.118	73	0.12	1848	0.12	1921	0.992	0.992	100	0.124
2.533-2.83	0.129	82	0.132	1675	0.132	1757	0.99	0.99	100	0.143
2.83-3.263	0.177	49	0.147	1512	0.148	1561	0.981	0.986	100	0.165
3.263-3.985	0.2	55	0.15	1285	0.152	1340	0.977	0.987	100	0.176
3.985-5.588	0.176	47	0.134	1013	0.136	1060	0.987	0.99	100	0.174
5.588-30.512	0.214	16	0.265	626	0.264	642	0.969	0.946	100	0.431

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