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- PDB-9dy5: The crystal structure of F182A CYP199A4 bound to 4-methylthiobenz... -

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Basic information

Entry
Database: PDB / ID: 9dy5
TitleThe crystal structure of F182A CYP199A4 bound to 4-methylthiobenzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 peroxygenase / sulfoxidation
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
4-methylsulfanylbenzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPodgorski, M.N. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Acs Catalysis / Year: 2025
Title: Comparing and Combining Alternative Strategies for Enhancing Cytochrome P450 Peroxygenase Activity
Authors: Podgorski, M.N. / Bell, S.G.
History
DepositionOct 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2963
Polymers44,5111
Non-polymers7852
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-24 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.153, 51.237, 78.412
Angle α, β, γ (deg.)90.00, 93.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 / CYP199A4


Mass: 44511.336 Da / Num. of mol.: 1 / Mutation: F182A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris HaA2 (phototrophic)
Gene: RPB_3613 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2IU02
#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-4MI / 4-methylsulfanylbenzoic acid


Mass: 168.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 1.99 Å3/Da / Density % sol: 38.16 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 100 mM Bis-Tris (adjusted to pH 5.0-5.75 with acetic acid), 0.2 M magnesium acetate, 20-32% PEG3350
PH range: 5.0-5.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95373 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.5→42.87 Å / Num. obs: 12221 / % possible obs: 99.4 % / Redundancy: 7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.08 / Rrim(I) all: 0.215 / Χ2: 1.02 / Net I/σ(I): 8.3 / Num. measured all: 85140
Reflection shellResolution: 2.5→2.6 Å / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.98 / Num. measured all: 9982 / Num. unique obs: 1387 / CC1/2: 0.854 / Rpim(I) all: 0.388 / Rrim(I) all: 1.054 / Χ2: 1 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→42.868 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2812 549 4.51 %
Rwork0.2372 --
obs0.2394 12181 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→42.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 54 68 3137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053170
X-RAY DIFFRACTIONf_angle_d0.5464331
X-RAY DIFFRACTIONf_dihedral_angle_d16.4021898
X-RAY DIFFRACTIONf_chiral_restr0.04471
X-RAY DIFFRACTIONf_plane_restr0.005576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.75160.45841220.34912898X-RAY DIFFRACTION99
2.7516-3.14960.3571580.28922866X-RAY DIFFRACTION99
3.1496-3.96770.24351470.21862906X-RAY DIFFRACTION99
3.9677-42.8680.22611220.19172962X-RAY DIFFRACTION98

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