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- PDB-9js9: Crystal structure of the CYP154C5 F92A/R114A/T248G/E282A variant ... -

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Basic information

Entry
Database: PDB / ID: 9js9
TitleCrystal structure of the CYP154C5 F92A/R114A/T248G/E282A variant from Nocardia farcinica
ComponentsCytochrome P450 monooxygenase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Monooxygenase / Metalloprotein
Function / homology
Function and homology information


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, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / TESTOSTERONE / Cytochrome P450 monooxygenase
Similarity search - Component
Biological speciesNocardia farcinica IFM 10152 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsQin, M.M. / Fan, S.X. / Cong, Z.Q. / Jiang, Y.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of the CYP154C5 F92A/R114A/T248G/E282A variant from Nocardia farcinica
Authors: Qin, M.M. / Fan, S.X. / Cong, Z.Q. / Jiang, Y.P.
History
DepositionSep 30, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Cytochrome P450 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0323
Polymers47,1271
Non-polymers9052
Water6,071337
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, eqlibrium between monomer and dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.648, 61.679, 68.164
Angle α, β, γ (deg.)90.00, 113.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 monooxygenase


Mass: 47126.664 Da / Num. of mol.: 1 / Mutation: F92A,R114A,T248G,E282A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia farcinica IFM 10152 (bacteria)
Gene: NFA_53110 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5YNS8
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-TES / TESTOSTERONE


Mass: 288.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris pH 6.0, 0.2M NaCl, 19% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.89→62.29 Å / Num. obs: 32821 / % possible obs: 96.7 % / Redundancy: 3.4 % / CC1/2: 0.864 / Rrim(I) all: 0.422 / Χ2: 0.92 / Net I/σ(I): 4.9
Reflection shellResolution: 1.89→1.99 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.195 / Num. unique obs: 4588 / CC1/2: 0.468 / Rpim(I) all: 0.795 / Χ2: 0.85

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
autoPROCdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J6B

4j6b


Resolution: 1.89→33.32 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2432 1993 6.1 %
Rwork0.2031 --
obs0.2055 32667 95.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→33.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3105 0 0 337 3442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043210
X-RAY DIFFRACTIONf_angle_d0.7784408
X-RAY DIFFRACTIONf_dihedral_angle_d18.2331151
X-RAY DIFFRACTIONf_chiral_restr0.046519
X-RAY DIFFRACTIONf_plane_restr0.005561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.930.38351360.31662030X-RAY DIFFRACTION89
1.93-1.980.30541370.2982060X-RAY DIFFRACTION91
1.98-2.040.29611390.26092168X-RAY DIFFRACTION94
2.04-2.110.29741420.25522174X-RAY DIFFRACTION97
2.11-2.180.28531410.23492250X-RAY DIFFRACTION98
2.18-2.270.28011490.22042261X-RAY DIFFRACTION98
2.27-2.370.23641500.20532247X-RAY DIFFRACTION98
2.38-2.50.29431450.21152232X-RAY DIFFRACTION99
2.5-2.660.2451440.20642250X-RAY DIFFRACTION97
2.66-2.860.21241450.20692197X-RAY DIFFRACTION97
2.86-3.150.26531440.1952193X-RAY DIFFRACTION95
3.15-3.60.2391450.18752241X-RAY DIFFRACTION97
3.61-4.540.17941400.14292225X-RAY DIFFRACTION96
4.54-33.320.17851360.1642146X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: -4.2307 Å / Origin y: -10.8711 Å / Origin z: -15.8652 Å
111213212223313233
T0.2133 Å20.0059 Å2-0.0612 Å2-0.1078 Å20.0013 Å2--0.0873 Å2
L0.3959 °20.0473 °20.2865 °2-1.8378 °20.2663 °2--0.8236 °2
S0.0363 Å °0.0429 Å °0.0368 Å °-0.3966 Å °-0.0478 Å °0.0634 Å °0.0453 Å °0.0157 Å °0.0231 Å °
Refinement TLS groupSelection details: all

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