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- PDB-9iy1: P450 BS beta mutant F46A -

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Basic information

Entry
Database: PDB / ID: 9iy1
TitleP450 BS beta mutant F46A
ComponentsFatty-acid peroxygenase
KeywordsOXIDOREDUCTASE / peroxygenases
Function / homology
Function and homology information


fatty-acid peroxygenase / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
: / Cytochrome P450, E-class, group I / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / PALMITIC ACID / Fatty-acid peroxygenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsGong, P.Q. / Gao, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Unexpected Activities of CYP152 Peroxygenases towards Non-carboxylic Substrates Reveal Novel Substrate Recognition Mechanism and Catalytic Versatility.
Authors: Jiang, Y. / Gong, P. / Li, Z. / Li, Z. / Li, Y. / Wang, B. / Huang, H. / Peng, W. / Gao, X. / Li, S.
History
DepositionJul 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 30, 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: Fatty-acid peroxygenase
B: Fatty-acid peroxygenase
C: Fatty-acid peroxygenase
D: Fatty-acid peroxygenase
E: Fatty-acid peroxygenase
F: Fatty-acid peroxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,95766
Polymers288,1076
Non-polymers9,85060
Water17,150952
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint-50 kcal/mol
Surface area98440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.420, 190.114, 226.571
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Components on special symmetry positions
IDModelComponents
11D-716-

HOH

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Fatty-acid peroxygenase / P450 BS beta / Cytochrome P450 152A1 / Cytochrome P450BsBeta / Fatty acid beta-hydroxylase


Mass: 48017.891 Da / Num. of mol.: 6 / Mutation: F46A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: cypC, CYP152A1, BSU02100 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O31440, fatty-acid peroxygenase

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Non-polymers , 6 types, 1012 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 952 / 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: 3.14 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.45M Li2SO4, 50mM MES, pH 5.8, 10% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.29→49.49 Å / Num. obs: 165978 / % possible obs: 97.45 % / Redundancy: 12.9 % / Biso Wilson estimate: 28.4 Å2 / CC1/2: 0.983 / Net I/σ(I): 1.47
Reflection shellResolution: 2.29→2.372 Å / Num. unique obs: 16442 / CC1/2: 0.636

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IZO

1izo


Resolution: 2.29→49.49 Å / SU ML: 0.2728 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.5898
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2403 1997 1.23 %
Rwork0.198 160142 -
obs0.1985 162139 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.06 Å2
Refinement stepCycle: LAST / Resolution: 2.29→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20192 0 651 952 21795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004121323
X-RAY DIFFRACTIONf_angle_d0.567128744
X-RAY DIFFRACTIONf_chiral_restr0.03792914
X-RAY DIFFRACTIONf_plane_restr0.00393687
X-RAY DIFFRACTIONf_dihedral_angle_d16.75918021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.340.2921230.25429929X-RAY DIFFRACTION84.67
2.34-2.410.31131410.247711215X-RAY DIFFRACTION95.77
2.41-2.480.30121400.239711199X-RAY DIFFRACTION95.68
2.48-2.560.31291410.23911305X-RAY DIFFRACTION96.46
2.56-2.650.3031410.239711356X-RAY DIFFRACTION97.07
2.65-2.750.29981430.241411450X-RAY DIFFRACTION97.32
2.75-2.880.27231440.22311479X-RAY DIFFRACTION97.74
2.88-3.030.24471430.216111536X-RAY DIFFRACTION98.1
3.03-3.220.26511450.215611630X-RAY DIFFRACTION98.75
3.22-3.470.25021470.202111705X-RAY DIFFRACTION99.25
3.47-3.820.23951470.178211755X-RAY DIFFRACTION99.39
3.82-4.370.16981470.158111776X-RAY DIFFRACTION99.41
4.37-5.50.18531480.156911873X-RAY DIFFRACTION99.42
5.51-49.490.21671470.182411934X-RAY DIFFRACTION97.6

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