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- PDB-9srj: Prenylated FMN oxidative maturase PhdC, PEG-bound -

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Basic information

Entry
Database: PDB / ID: 9srj
TitlePrenylated FMN oxidative maturase PhdC, PEG-bound
ComponentsPyridoxamine 5'-phosphate oxidase putative domain-containing protein
KeywordsFLAVOPROTEIN / prFMN / oxidative maturation / PhdC
Function / homologyDI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Pyridoxamine 5'-phosphate oxidase putative domain-containing protein
Function and homology information
Biological speciesMycolicibacterium fortuitum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsBox, H.G. / Leys, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Proteins / Year: 2025
Title: Structure and Mechanism of PhdC, a Prenylated-Flavin Maturase.
Authors: Whittall, D.R. / Box, H.G. / Payne, K.A.P. / Marshall, S.A. / Leys, D.
History
DepositionSep 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,0389
Polymers36,5842
Non-polymers4547
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-30 kcal/mol
Surface area12490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.253, 121.253, 121.253
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

21B-360-

HOH

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Components

#1: Protein Pyridoxamine 5'-phosphate oxidase putative domain-containing protein


Mass: 18291.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal polyhistidine tag / Source: (gene. exp.) Mycolicibacterium fortuitum (bacteria) / Gene: XA26_16660 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0N9XAG5
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.03 Å3/Da / Density % sol: 39.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M Sodium acetate, pH 4.6, 8 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.42→49.5 Å / Num. obs: 55801 / % possible obs: 100 % / Redundancy: 37 % / CC1/2: 1 / Net I/σ(I): 26.2
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 16.5 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2807 / CC1/2: 0.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
PDB_EXTRACTdata extraction
Cootmodel building
AutoProcessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→38.34 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2036 2022 3.63 %
Rwork0.1811 --
obs0.1819 55721 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→38.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2302 0 28 187 2517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052428
X-RAY DIFFRACTIONf_angle_d0.8683295
X-RAY DIFFRACTIONf_dihedral_angle_d15.773902
X-RAY DIFFRACTIONf_chiral_restr0.079378
X-RAY DIFFRACTIONf_plane_restr0.011435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.460.39281420.3863732X-RAY DIFFRACTION98
1.46-1.490.36561250.34713820X-RAY DIFFRACTION100
1.5-1.540.29751490.27453832X-RAY DIFFRACTION100
1.54-1.590.241450.22693833X-RAY DIFFRACTION100
1.59-1.650.22481220.21373804X-RAY DIFFRACTION100
1.65-1.710.2141830.19683788X-RAY DIFFRACTION100
1.71-1.790.21881510.19033814X-RAY DIFFRACTION100
1.79-1.880.23671410.21493835X-RAY DIFFRACTION100
1.88-20.21961500.17483822X-RAY DIFFRACTION100
2-2.150.19081440.17823823X-RAY DIFFRACTION100
2.16-2.370.20531390.18783855X-RAY DIFFRACTION100
2.37-2.720.20891400.18093880X-RAY DIFFRACTION100
2.72-3.420.20841340.18063888X-RAY DIFFRACTION100
3.42-38.340.17331570.15123973X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.9396-1.26821.93712.0759-1.12781.201-0.03080.527-0.1823-0.3252-0.1129-0.07570.17350.1550.14480.28410.01410.08610.19460.0180.17665.1856-37.8635-53.4996
21.70490.5279-0.44821.4178-0.2830.5114-0.0526-0.0258-0.1071-0.1487-0.094-0.10950.19620.12640.12180.231-0.01670.07010.16420.03170.1941.7635-40.1557-43.6182
31.42381.2487-0.5912.6837-0.91652.11530.0457-0.06930.05310.0636-0.1420.07370.09670.00310.1140.1989-0.020.06430.16140.00740.1936-3.128-37.5149-40.466
43.1251.8156-0.10811.9787-0.6271.7864-0.0613-0.04630.1654-0.2018-0.03090.05620.0288-0.00820.09240.23050.00750.0480.17510.00150.1834-0.9613-36.1258-45.0774
52.1307-0.1752-0.11552.662-0.21481.0029-0.01950.167-0.3874-0.1684-0.14830.05620.51420.11520.13680.41680.02950.14770.20420.03030.32847.6976-49.7614-47.8534
62.09670.9417-0.90514.2988-2.08843.84750.1541-0.2781-0.07850.1935-0.0883-0.0121-0.66480.83960.0860.3906-0.2219-0.10210.54050.04360.291612.5398-21.5285-26.6742
72.8731.00880.26952.63850.14522.7085-0.0502-0.12250.08490.1946-0.1317-0.0383-0.39150.18840.13640.2427-0.068-0.00770.22070.00670.18281.8702-23.6005-30.234
82.9957-0.6414-0.32752.62620.38663.2540.0538-0.03990.14910.1534-0.19630.1279-0.1972-0.20820.20590.2143-0.040.0240.1978-0.03060.2175-4.301-26.4509-30.8576
92.8723-0.74420.70472.4704-0.4381.47390.12980.0291-0.10270.2958-0.35310.1116-0.09020.13770.15710.273-0.0834-0.00390.28270.05390.23885.1759-32.5817-27.5052
102.57630.4891-0.09133.4659-0.46652.83240.0967-0.04850.03850.455-0.4220.0551-0.260.08790.25960.3054-0.0785-0.02020.30480.00490.16850.9815-26.3126-24.5475
112.3898-0.7997-1.28384.24941.6085.31970.23420.07180.0224-0.4468-0.26090.5009-1.22030.21560.13520.44-0.1021-0.0010.290.03760.271410.9674-19.9912-39.152
124.36420.0713-1.60683.773-1.68945.4885-0.0339-0.83161.4730.4491-0.10930.0457-1.61570.79440.21810.8312-0.0648-0.0430.4422-0.20070.54282.0446-11.2519-22.6259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 63 )
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 93 )
4X-RAY DIFFRACTION4chain 'A' and (resid 94 through 124 )
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 155 )
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 22 )
7X-RAY DIFFRACTION7chain 'B' and (resid 23 through 63 )
8X-RAY DIFFRACTION8chain 'B' and (resid 64 through 82 )
9X-RAY DIFFRACTION9chain 'B' and (resid 83 through 93 )
10X-RAY DIFFRACTION10chain 'B' and (resid 94 through 116 )
11X-RAY DIFFRACTION11chain 'B' and (resid 117 through 137 )
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 153 )

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