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- PDB-9dy9: The crystal structure of F182A CYP199A4 bound to 4-methoxybenzoic acid -

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Basic information

Entry
Database: PDB / ID: 9dy9
TitleThe crystal structure of F182A CYP199A4 bound to 4-methoxybenzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 peroxygenase / O-demethylation
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-METHOXYBENZOIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.672 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)45,3154
Polymers44,5111
Non-polymers8043
Water13,007722
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-32 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.892, 51.533, 77.917
Angle α, β, γ (deg.)90.00, 94.00, 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-ANN / 4-METHOXYBENZOIC ACID / P-ANISIC ACID


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 722 / 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: 2.02 Å3/Da / Density % sol: 39.11 %
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: Sep 27, 2023
RadiationMonochromator: Double-crystal Si(111) water-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.67→44.78 Å / Num. obs: 41026 / % possible obs: 99.5 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.056 / Rrim(I) all: 0.147 / Χ2: 0.58 / Net I/σ(I): 7.9 / Num. measured all: 283256
Reflection shellResolution: 1.67→1.7 Å / % possible obs: 98.2 % / Redundancy: 6.5 % / Rmerge(I) obs: 1.319 / Num. measured all: 13474 / Num. unique obs: 2061 / CC1/2: 0.548 / Rpim(I) all: 0.546 / Rrim(I) all: 1.431 / Χ2: 0.56 / Net I/σ(I) obs: 1.1

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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: 1.672→40.029 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.192 2002 4.88 %
Rwork0.1425 --
obs0.1449 40999 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.672→40.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 55 722 3792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063227
X-RAY DIFFRACTIONf_angle_d0.8214417
X-RAY DIFFRACTIONf_dihedral_angle_d23.0591187
X-RAY DIFFRACTIONf_chiral_restr0.051478
X-RAY DIFFRACTIONf_plane_restr0.006591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6721-1.7140.30841380.27472740X-RAY DIFFRACTION98
1.714-1.76030.27861460.21542754X-RAY DIFFRACTION100
1.7603-1.81210.2331430.19262784X-RAY DIFFRACTION100
1.8121-1.87060.20691380.16592798X-RAY DIFFRACTION100
1.8706-1.93750.21771380.16462763X-RAY DIFFRACTION99
1.9375-2.0150.21771500.16012779X-RAY DIFFRACTION99
2.015-2.10670.21081380.14552756X-RAY DIFFRACTION99
2.1067-2.21780.22421500.13992751X-RAY DIFFRACTION98
2.2178-2.35670.18451400.13682804X-RAY DIFFRACTION99
2.3567-2.53870.20361370.13732773X-RAY DIFFRACTION100
2.5387-2.79410.19811510.14222811X-RAY DIFFRACTION100
2.7941-3.19820.18391440.13272805X-RAY DIFFRACTION100
3.1982-4.02880.14081430.11182808X-RAY DIFFRACTION99
4.0288-40.0290.16321460.12482871X-RAY DIFFRACTION99

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