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- PDB-7r8t: High-resolution crystal structure of CYP199A4 bound to 4-ethylben... -

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Basic information

Entry
Database: PDB / ID: 7r8t
TitleHigh-resolution crystal structure of CYP199A4 bound to 4-ethylbenzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / 4-ethylbenzoic acid / hydroxylation / desaturation / epoxidation
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-ethylbenzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.366 Å
AuthorsPodgorski, M.N. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: High-resolution crystal structure of CYP199A4 bound to 4-ethylbenzoic acid
Authors: Podgorski, M.N. / Bell, S.G.
History
DepositionJun 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)45,3904
Polymers44,5871
Non-polymers8023
Water10,016556
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-37 kcal/mol
Surface area15060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.270, 51.400, 79.197
Angle α, β, γ (deg.)90.000, 91.950, 90.000
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 (strain HaA2) (phototrophic)
Strain: HaA2 / 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-EGM / 4-ethylbenzoic acid


Mass: 150.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O2 / 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.: 556 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 39.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2 M magnesium acetate, 100 mM Bis-Tris (adjusted with acetic acid to pH 5.0-5.75), 20-32% w/v 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: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2020
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: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.366→44.244 Å / Num. obs: 74710 / % possible obs: 99 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.032 / Rrim(I) all: 0.082 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.37-1.396.60.7082418936630.7870.2930.7681.792
7.23-44.246.40.04534645440.9980.0190.0493098.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.83 Å44.24 Å
Translation5.83 Å44.24 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UVB

5uvb


Resolution: 1.366→44.244 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1804 2002 2.68 %
Rwork0.1531 72678 -
obs0.1538 74680 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.06 Å2 / Biso mean: 18.3624 Å2 / Biso min: 8.83 Å2
Refinement stepCycle: final / Resolution: 1.366→44.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 55 556 3632
Biso mean--11.18 29.98 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063205
X-RAY DIFFRACTIONf_angle_d0.9424383
X-RAY DIFFRACTIONf_chiral_restr0.077475
X-RAY DIFFRACTIONf_plane_restr0.006584
X-RAY DIFFRACTIONf_dihedral_angle_d11.6411887
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3661-1.40030.25241320.2521485894
1.4003-1.43820.26221360.2293517999
1.4382-1.48050.2021410.201513299
1.4805-1.52830.19541430.1781518399
1.5283-1.58290.23541480.1689516599
1.5829-1.64630.18851420.1551518799
1.6463-1.72120.17831420.1556518699
1.7212-1.81190.18431400.14935200100
1.8119-1.92550.18191540.15185238100
1.9255-2.07410.18911440.15275214100
2.0741-2.28280.18331460.14525245100
2.2828-2.61310.16021440.15155284100
2.6131-3.29210.18761420.15225265100
3.2921-44.2440.15611480.1335534299

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