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- PDB-9y34: Cytochrome P450 158A2 (CYP158A2) variant P354L -

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Basic information

Entry
Database: PDB / ID: 9y34
TitleCytochrome P450 158A2 (CYP158A2) variant P354L
ComponentsBiflaviolin synthase CYP158A2
KeywordsOXIDOREDUCTASE / cytochrome P450 / flaviolin
Function / homology
Function and homology information


biflaviolin synthase / pigment 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, 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 / Biflaviolin synthase CYP158A2
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsGable, J.A. / Follmer, A.H. / Poulos, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM57353 United States
CitationJournal: To Be Published
Title: Proximal Push in Cytochromes P450
Authors: Gable, J.A. / Follmer, A.H. / Poulos, T.L.
History
DepositionSep 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Biflaviolin synthase CYP158A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0412
Polymers44,4251
Non-polymers6161
Water6,774376
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.550, 67.280, 104.601
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Biflaviolin synthase CYP158A2 / Cytochrome P450 158A2 / CYP158A2


Mass: 44424.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: cyp158a2, SCO1207 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FCA6, biflaviolin synthase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: The protein sample had a concentration of 20 mg/mL in 20 mM Tris pH 7.4. The well solution was 0.1 M Bis-Tris pH 6.5 and 25% PEG 3350. The crystals were grown in a 1:1 drop ratio of protein:well

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.879→50.42 Å / Num. obs: 33807 / % possible obs: 99.93 % / Redundancy: 6.9 % / Biso Wilson estimate: 13.75 Å2 / CC1/2: 0.977 / Net I/σ(I): 6.95
Reflection shellResolution: 1.879→1.93 Å / Mean I/σ(I) obs: 3.85 / Num. unique obs: 19173 / CC1/2: 0.909

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→50.42 Å / SU ML: 0.1731 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 17.418
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1949 1678 4.97 %
Rwork0.1622 32111 -
obs0.1638 33789 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.63 Å2
Refinement stepCycle: LAST / Resolution: 1.88→50.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3056 0 43 376 3475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01313190
X-RAY DIFFRACTIONf_angle_d1.37074365
X-RAY DIFFRACTIONf_chiral_restr0.0787481
X-RAY DIFFRACTIONf_plane_restr0.0257579
X-RAY DIFFRACTIONf_dihedral_angle_d13.35221193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.930.23051290.19592636X-RAY DIFFRACTION99.86
1.93-20.22431520.17882609X-RAY DIFFRACTION99.89
2-2.070.22851470.17722624X-RAY DIFFRACTION99.93
2.07-2.150.21821450.16382633X-RAY DIFFRACTION99.89
2.15-2.250.21221250.15642664X-RAY DIFFRACTION99.89
2.25-2.370.19371460.15532634X-RAY DIFFRACTION100
2.37-2.520.22051640.16422634X-RAY DIFFRACTION99.93
2.52-2.710.19811360.16642675X-RAY DIFFRACTION100
2.71-2.980.20621430.16142682X-RAY DIFFRACTION99.96
2.98-3.410.17751270.1582708X-RAY DIFFRACTION100
3.41-4.30.17231360.14792732X-RAY DIFFRACTION100
4.3-50.420.16191280.16332880X-RAY DIFFRACTION99.97

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