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- PDB-8vok: The crystal structure of wild-type CYP199A4 bound to 4-hydroxyben... -

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Basic information

Entry
Database: PDB / ID: 8vok
TitleThe crystal structure of wild-type CYP199A4 bound to 4-hydroxybenzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / catalytic product
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 / P-HYDROXYBENZOIC ACID / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.538 Å
AuthorsPodgorski, M.N. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: The crystal structure of wild-type CYP199A4 bound to 4-hydroxybenzoic acid
Authors: Podgorski, M.N. / Bell, S.G.
History
DepositionJan 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 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)45,3774
Polymers44,5871
Non-polymers7903
Water8,899494
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.366, 51.309, 78.822
Angle α, β, γ (deg.)90.00, 92.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 / CYP199A4


Mass: 44587.430 Da / Num. of mol.: 1
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-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3 / 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.: 494 / 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: 2.01 Å3/Da / Density % sol: 38.83 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: The crystallization buffer was 100 mM Bis-Tris buffer (adjusted to pH 5.0-5.75 with acetic acid), 0.2 M magnesium acetate and 20-32% PEG 3350
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: 0.95372 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 12, 2020
RadiationMonochromator: Double-crystal Si(111) water-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.538→44.34 Å / Num. obs: 52720 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.029 / Rrim(I) all: 0.075 / Χ2: 0.54 / Net I/σ(I): 13.7
Reflection shellResolution: 1.54→1.56 Å / % possible obs: 97.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 1.026 / Num. measured all: 16737 / Num. unique obs: 2506 / CC1/2: 0.772 / Rpim(I) all: 0.42 / Rrim(I) all: 1.111 / Χ2: 0.53 / Net I/σ(I) obs: 1.5

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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: 1.538→42.992 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1879 1997 3.79 %
Rwork0.1622 --
obs0.1632 52689 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.538→42.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 54 494 3569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053189
X-RAY DIFFRACTIONf_angle_d0.8154360
X-RAY DIFFRACTIONf_dihedral_angle_d23.61172
X-RAY DIFFRACTIONf_chiral_restr0.049474
X-RAY DIFFRACTIONf_plane_restr0.005580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.538-1.57630.29711400.27733549X-RAY DIFFRACTION98
1.5763-1.61890.23421410.23263605X-RAY DIFFRACTION100
1.6189-1.66660.22661400.21013576X-RAY DIFFRACTION100
1.6666-1.72040.22911510.20173612X-RAY DIFFRACTION100
1.7204-1.78190.24171410.19043619X-RAY DIFFRACTION100
1.7819-1.85320.23911410.18013588X-RAY DIFFRACTION100
1.8532-1.93750.18821410.17253638X-RAY DIFFRACTION100
1.9375-2.03970.21141390.16323588X-RAY DIFFRACTION100
2.0397-2.16750.19961410.15283609X-RAY DIFFRACTION100
2.1675-2.33480.19461490.1543680X-RAY DIFFRACTION100
2.3348-2.56980.17571420.15633584X-RAY DIFFRACTION100
2.5698-2.94150.17391330.15733677X-RAY DIFFRACTION100
2.9415-3.70570.16891510.1423626X-RAY DIFFRACTION100
3.7057-42.9920.15431470.14443741X-RAY DIFFRACTION100

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