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- PDB-9jqm: X-ray structure of cytochrome P450 OleT from Lacicoccus alkaliphi... -

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Basic information

Entry
Database: PDB / ID: 9jqm
TitleX-ray structure of cytochrome P450 OleT from Lacicoccus alkaliphilus in complex with icosanoic acid
ComponentsFatty-acid peroxygenase
KeywordsOXIDOREDUCTASE / Decarboxylation / Hydroxylation / Cytochrome P450 / CYP152 / Monooxygenase / Decarboxylase
Function / homology
Function and homology information


sterol metabolic process / 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
icosanoic acid / PROTOPORPHYRIN IX CONTAINING FE / Fatty-acid peroxygenase
Similarity search - Component
Biological speciesLacicoccus alkaliphilus DSM 16010 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsPhaisan, S. / Phintha, A. / Trisrivirat, D. / Charoenpol, A. / Tanaka, H. / Kurisu, G. / Watthaisong, P. / Sucharitakul, J. / Chaiyen, P.
Funding support Thailand, 4items
OrganizationGrant numberCountry
Vidyasirimedhi Institute of Science and Technology (VISTEC) Thailand
Program Management Unit for Human Resources & Institutional Development (PMU-B) Research and InnovationB05F640089 Thailand
Thailand Science Research and InnovationFRB670026/0457 Thailand
KasikornBank Public Company Limited Thailand
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Unique structural features define the decarboxylation activity of a CYP152 fatty acid decarboxylase from Lacicoccus alkaliphilus.
Authors: Phaisan, S. / Phintha, A. / Trisrivirat, D. / Lawan, N. / Sucharitakul, J. / Charoenpol, A. / Watthaisong, P. / Tanaka, H. / Kurisu, G. / Chaiyen, P.
History
DepositionSep 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Fatty-acid peroxygenase
A: Fatty-acid peroxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,63812
Polymers100,2282
Non-polymers2,41110
Water10,034557
1
B: Fatty-acid peroxygenase
hetero molecules

B: Fatty-acid peroxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,63812
Polymers100,2282
Non-polymers2,41110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_565x,-y+1,-z+1/21
2
A: Fatty-acid peroxygenase
hetero molecules

A: Fatty-acid peroxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,63812
Polymers100,2282
Non-polymers2,41110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_565x,-y+1,-z+1/21
Unit cell
Length a, b, c (Å)82.799, 188.859, 198.313
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2

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Components

#1: Protein Fatty-acid peroxygenase


Mass: 50113.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lacicoccus alkaliphilus DSM 16010 (bacteria)
Gene: SAMN02745189_00740 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1M7CBV6
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DCR / icosanoic acid


Mass: 312.530 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H40O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H2O
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: 3.87 Å3/Da / Density % sol: 68.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: Enzyme 10 mg/mL and icosanoic acid 1 mM in 0.1 M NaCl, 0.1 M HEPES pH7.5 and 3.5 M Sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 58908 / % possible obs: 99 % / Redundancy: 3.5 % / Biso Wilson estimate: 24.44 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.51
Reflection shellResolution: 2.44→2.59 Å / Redundancy: 6.89 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 1.62 / Num. unique obs: 9086 / CC1/2: 0.791 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→42.63 Å / SU ML: 0.3955 / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 25.0656
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2296 5578 5.04 %
Rwork0.182 105113 -
obs0.1844 57875 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.44→42.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6906 0 166 557 7629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00867240
X-RAY DIFFRACTIONf_angle_d1.01699777
X-RAY DIFFRACTIONf_chiral_restr0.05391005
X-RAY DIFFRACTIONf_plane_restr0.00891251
X-RAY DIFFRACTIONf_dihedral_angle_d12.95211012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.470.36431580.373013X-RAY DIFFRACTION84.76
2.47-2.50.3911820.33743523X-RAY DIFFRACTION99.95
2.5-2.530.36461900.32653528X-RAY DIFFRACTION99.95
2.53-2.560.34311890.28783587X-RAY DIFFRACTION99.89
2.56-2.590.31271870.27493491X-RAY DIFFRACTION99.92
2.59-2.630.33111900.26193528X-RAY DIFFRACTION100
2.63-2.670.34771870.2633562X-RAY DIFFRACTION100
2.67-2.710.29831870.24773519X-RAY DIFFRACTION99.95
2.71-2.750.25731870.25533544X-RAY DIFFRACTION100
2.75-2.790.32631830.25683522X-RAY DIFFRACTION100
2.79-2.840.32721910.26743556X-RAY DIFFRACTION99.92
2.84-2.890.30621880.26353526X-RAY DIFFRACTION99.87
2.89-2.950.33811890.24453560X-RAY DIFFRACTION99.95
2.95-3.010.26011830.21773486X-RAY DIFFRACTION99.95
3.01-3.070.29281890.20623554X-RAY DIFFRACTION99.95
3.07-3.150.25531910.20183568X-RAY DIFFRACTION99.87
3.15-3.220.25211870.19323513X-RAY DIFFRACTION99.97
3.22-3.310.2641890.18963583X-RAY DIFFRACTION99.97
3.31-3.410.22431880.18613523X-RAY DIFFRACTION99.68
3.41-3.520.20651840.18153476X-RAY DIFFRACTION99.73
3.52-3.640.23981860.17193563X-RAY DIFFRACTION99.42
3.64-3.790.18871840.16443481X-RAY DIFFRACTION98.79
3.79-3.960.2191890.16243512X-RAY DIFFRACTION99.06
3.96-4.170.19241840.15873450X-RAY DIFFRACTION98.16
4.17-4.430.21211860.15073481X-RAY DIFFRACTION97.71
4.43-4.770.20751900.13713487X-RAY DIFFRACTION98.13
4.77-5.250.18151860.14763513X-RAY DIFFRACTION99.68
5.25-6.010.22251860.18013522X-RAY DIFFRACTION99.52
6.01-7.570.20921840.18043494X-RAY DIFFRACTION98.37
7.57-42.630.20651840.16353448X-RAY DIFFRACTION97.32

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