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- PDB-9dxw: The crystal structure of F182A CYP199A4 bound to 4-t-butylbenzoic acid -

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Basic information

Entry
Database: PDB / ID: 9dxw
TitleThe crystal structure of F182A CYP199A4 bound to 4-t-butylbenzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 peroxygenase mutant
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-~{tert}-butylbenzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 11, 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)45,3424
Polymers44,5111
Non-polymers8303
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-36 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.689, 51.337, 78.541
Angle α, β, γ (deg.)90.00, 93.14, 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-5R0 / 4-~{tert}-butylbenzoic acid


Mass: 178.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14O2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 377 / 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: 39.14 %
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: MX2 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 31, 2023
RadiationMonochromator: Double-crystal Si(111) liquid nitrogen cooled (DC) or channel-cut Si(111) liquid nitrogen cooled (CC)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.05→44.622 Å / Num. obs: 22497 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.988 / Rmerge(I) obs: 0.252 / Rpim(I) all: 0.109 / Rrim(I) all: 0.276 / Χ2: 1.01 / Net I/σ(I): 6.1
Reflection shellResolution: 2.05→2.11 Å / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 1.289 / Num. measured all: 10391 / Num. unique obs: 1727 / CC1/2: 0.621 / Rpim(I) all: 0.574 / Rrim(I) all: 1.414 / Χ2: 0.87 / Net I/σ(I) obs: 1.6

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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: 2.05→44.622 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2351 1084 4.83 %
Rwork0.1944 --
obs0.1963 22429 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→44.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 57 377 3449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033194
X-RAY DIFFRACTIONf_angle_d0.6164368
X-RAY DIFFRACTIONf_dihedral_angle_d24.5681180
X-RAY DIFFRACTIONf_chiral_restr0.041473
X-RAY DIFFRACTIONf_plane_restr0.005581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.14330.30811400.26632653X-RAY DIFFRACTION100
2.1433-2.25630.30291220.24612656X-RAY DIFFRACTION100
2.2563-2.39770.28311180.22392658X-RAY DIFFRACTION100
2.3977-2.58280.23821330.21342663X-RAY DIFFRACTION100
2.5828-2.84270.25011530.21022648X-RAY DIFFRACTION100
2.8427-3.25390.24831670.19092632X-RAY DIFFRACTION100
3.2539-4.09910.21331230.16542696X-RAY DIFFRACTION99
4.0991-44.6220.1831280.16432739X-RAY DIFFRACTION99

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