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- PDB-9nk1: Prenylated-FMN maturase PhdC from Mycolicibacterium fortuitum bou... -

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Basic information

Entry
Database: PDB / ID: 9nk1
TitlePrenylated-FMN maturase PhdC from Mycolicibacterium fortuitum bound to flavin mononucleotide
ComponentsPyridoxamine 5'-phosphate oxidase putative domain-containing protein
KeywordsFLAVOPROTEIN / FMN / Maturase / homodimer / beta-sandwhich
Function / homologyFLAVIN MONONUCLEOTIDE / Pyridoxamine 5'-phosphate oxidase putative domain-containing protein
Function and homology information
Biological speciesMycolicibacterium fortuitum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsKilde, I.R. / Koutmos, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2203729 United States
CitationJournal: 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
DepositionFeb 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyridoxamine 5'-phosphate oxidase putative domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3465
Polymers18,7081
Non-polymers6374
Water2,414134
1
A: Pyridoxamine 5'-phosphate oxidase putative domain-containing protein
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)38,69110
Polymers37,4162
Non-polymers1,2758
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area5710 Å2
ΔGint-52 kcal/mol
Surface area12700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.039, 75.032, 79.746
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#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) / Gene: XA26_16660 / Plasmid: pCDFduet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: A0A0N9XAG5

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Non-polymers , 5 types, 138 molecules

#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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: 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
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1:2 protein (20mM bistris pH 7.2, 200mM KCl, 1mM MnCl2, 5% glycerol +FMN reconstitution) 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2024
RadiationMonochromator: Liquid nitrogen-cooled double-crystal Si(111) monochromator with a 0.01% energy bandpass
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.23→47.97 Å / Num. obs: 44741 / % possible obs: 84.2 % / Redundancy: 5.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.015 / Rrim(I) all: 0.038 / Χ2: 0.73 / Net I/σ(I): 18.3
Reflection shellResolution: 1.23→1.25 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1834 / CC1/2: 0.508 / Rpim(I) all: 0.466 / Rrim(I) all: 0.733 / Χ2: 0.79 / % possible all: 32.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
Blu-Icedata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.23→47.965 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.79 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.036
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1481 2174 4.932 %
Rwork0.1308 41905 -
all0.132 --
obs-44079 83.882 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.907 Å2
Baniso -1Baniso -2Baniso -3
1--2.302 Å20 Å20 Å2
2--4.46 Å20 Å2
3----2.158 Å2
Refinement stepCycle: LAST / Resolution: 1.23→47.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 41 134 1357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0121265
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161182
X-RAY DIFFRACTIONr_angle_refined_deg2.141.8451722
X-RAY DIFFRACTIONr_angle_other_deg0.771.772715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6455155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.901515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.07610205
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.8491058
X-RAY DIFFRACTIONr_chiral_restr0.1240.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021526
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02294
X-RAY DIFFRACTIONr_nbd_refined0.2280.2222
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.21079
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2616
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2684
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.130.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0680.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.25
X-RAY DIFFRACTIONr_nbd_other0.1870.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.120.229
X-RAY DIFFRACTIONr_mcbond_it5.871.642617
X-RAY DIFFRACTIONr_mcbond_other5.7911.64617
X-RAY DIFFRACTIONr_mcangle_it7.8042.95773
X-RAY DIFFRACTIONr_mcangle_other7.8432.958774
X-RAY DIFFRACTIONr_scbond_it9.152.071648
X-RAY DIFFRACTIONr_scbond_other8.9222.061641
X-RAY DIFFRACTIONr_scangle_it12.8553.612949
X-RAY DIFFRACTIONr_scangle_other12.5943.589944
X-RAY DIFFRACTIONr_lrange_it17.30219.2121409
X-RAY DIFFRACTIONr_lrange_other16.20618.1211385
X-RAY DIFFRACTIONr_rigid_bond_restr6.8932447
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.23-1.2620.33680.2712180.27338230.90.91533.63850.255
1.262-1.2960.236970.22916190.2337680.8670.94845.54140.212
1.296-1.3340.18990.19819590.19736520.980.9756.35270.18
1.334-1.3750.211140.17822340.17935160.9680.9766.78040.157
1.375-1.420.2151410.16826090.17134410.9770.96779.91860.144
1.42-1.470.1481780.14429520.14433070.9780.98394.64770.121
1.47-1.5250.1651560.12830220.1332340.9830.99298.26840.109
1.525-1.5880.1421650.11928850.1230820.9880.99498.96170.103
1.588-1.6580.1521330.10428350.10629810.9860.99599.56390.09
1.658-1.7390.1361300.10427100.10628600.9880.99599.30070.092
1.739-1.8330.1471170.10725450.10927000.9810.99498.59260.098
1.833-1.9440.121210.10324370.10425650.9910.99599.72710.097
1.944-2.0780.1541130.10923180.11124350.9890.99499.83570.106
2.078-2.2440.131960.10921530.1122510.9910.99499.91120.109
2.244-2.4580.1371040.1119620.11220730.9890.99399.66230.114
2.458-2.7470.1441130.12317700.12419160.9870.9998.27770.131
2.747-3.170.14970.12615780.12716750.9870.991000.14
3.17-3.8780.118730.1413800.13914530.990.9871000.164
3.878-5.4670.19300.14210750.14311310.9820.98897.70110.17
5.467-47.9650.194290.2136420.2126780.9830.97698.96760.26

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