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- PDB-9nk3: Prenylated-FMN maturase PhdC E45A mutant from Mycolicibacterium f... -

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Basic information

Entry
Database: PDB / ID: 9nk3
TitlePrenylated-FMN maturase PhdC E45A mutant from Mycolicibacterium fortuitum (apo)
ComponentsPyridoxamine 5'-phosphate oxidase putative domain-containing protein
KeywordsFLAVOPROTEIN / Maturase / homodimer / beta-sandwhich / prFMN
Function / homologyPyridoxamine 5'-phosphate oxidase putative domain-containing protein
Function and homology information
Biological speciesMycolicibacterium fortuitum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsKilde, I.R. / Koutmos, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 2203729 United States
National Science Foundation (NSF, United States)CHE 1904759 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)18,9776
Polymers18,6501
Non-polymers3275
Water2,486138
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)37,95512
Polymers37,3002
Non-polymers65510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area4910 Å2
ΔGint2 kcal/mol
Surface area13530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.801, 75.605, 80.895
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222

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Components

#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) / Gene: XA26_16660 / Plasmid: pCDFduet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / 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: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 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 KCl 1mM MnCl2).
PH range: 7.2-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.729 Å
DetectorType: DECTRIS EIGER2 XE CdTe 16M / Detector: PIXEL / Date: Oct 11, 2024
RadiationMonochromator: 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 wavelengthWavelength: 0.729 Å / Relative weight: 1
ReflectionResolution: 1.32→55.24 Å / Num. obs: 36263 / % possible obs: 83.9 % / Redundancy: 8.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.02 / Rrim(I) all: 0.063 / Χ2: 0.98 / Net I/σ(I): 18.8
Reflection shellResolution: 1.32→1.34 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1091 / CC1/2: 0.767 / Rpim(I) all: 0.269 / Rrim(I) all: 0.521 / Χ2: 0.92 / % possible all: 50.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→48.134 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.475 / SU ML: 0.027 / Cross valid method: FREE R-VALUE / ESU R: 0.043 / ESU R Free: 0.042
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1456 1752 4.831 %
Rwork0.1204 34511 -
all0.122 --
obs-36263 83.54 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.124 Å2
Baniso -1Baniso -2Baniso -3
1--2.065 Å2-0 Å2-0 Å2
2--2.447 Å2-0 Å2
3----0.382 Å2
Refinement stepCycle: LAST / Resolution: 1.32→48.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 21 138 1342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0121262
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161207
X-RAY DIFFRACTIONr_angle_refined_deg2.1371.8471711
X-RAY DIFFRACTIONr_angle_other_deg0.751.762770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3055161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.114516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.31810206
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.3681057
X-RAY DIFFRACTIONr_chiral_restr0.1090.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021534
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02300
X-RAY DIFFRACTIONr_nbd_refined0.2270.2203
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.21049
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2605
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2716
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0040.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0650.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4230.216
X-RAY DIFFRACTIONr_nbd_other0.2920.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.110.225
X-RAY DIFFRACTIONr_mcbond_it6.191.562635
X-RAY DIFFRACTIONr_mcbond_other6.1891.566636
X-RAY DIFFRACTIONr_mcangle_it8.5132.803799
X-RAY DIFFRACTIONr_mcangle_other8.5422.809800
X-RAY DIFFRACTIONr_scbond_it10.4612.025627
X-RAY DIFFRACTIONr_scbond_other10.4552.028628
X-RAY DIFFRACTIONr_scangle_it14.5583.504912
X-RAY DIFFRACTIONr_scangle_other14.553.506913
X-RAY DIFFRACTIONr_lrange_it18.02620.4731351
X-RAY DIFFRACTIONr_lrange_other17.15219.6321327
X-RAY DIFFRACTIONr_rigid_bond_restr5.35432469
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
1.32-1.3540.195870.20215140.20231460.9630.9750.890.187
1.354-1.3910.211030.18216850.18431140.970.97157.41810.162
1.391-1.4320.201880.15820160.1630100.9650.97969.90030.139
1.432-1.4760.17870.13318930.13429070.980.98668.11150.116
1.476-1.5240.1641050.12420030.12628370.9730.98874.30380.108
1.524-1.5770.1511220.10623930.10927580.9820.99191.18930.094
1.577-1.6370.1591080.09924910.10226300.9820.99398.82130.091
1.637-1.7040.1211130.08424590.08625720.9920.9961000.078
1.704-1.7790.1381290.07921820.08224390.9870.99694.75190.075
1.779-1.8660.1111110.07722410.07823520.9920.9971000.074
1.866-1.9670.1281000.0917000.09222570.990.99579.75190.087
1.967-2.0860.134980.10617540.10721160.9860.99487.52360.107
2.086-2.230.13900.10618980.10719880.9890.9941000.109
2.23-2.4080.161830.10716370.1118810.9830.99391.44070.112
2.408-2.6370.134770.10816500.10917270.9870.9931000.116
2.637-2.9470.146740.12313310.12515590.9890.99190.12190.136
2.947-3.4010.154610.13413290.13513900.9850.9891000.152
3.401-4.160.132350.1289120.12812000.990.9978.91670.148
4.16-5.8610.12520.138920.139450.9940.99299.89420.162
5.861-48.1340.252280.2415300.2425670.9630.97198.41270.32

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