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- PDB-8d1c: Crystal structure of T252E-CYP199A4 in complex with 4-(Trifluorom... -

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Basic information

Entry
Database: PDB / ID: 8d1c
TitleCrystal structure of T252E-CYP199A4 in complex with 4-(Trifluoromethoxy)benzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / cytochrome / bacterial P450 / 4-trifluoromethoxybenzoic acid
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 / 4-(trifluoromethoxy)benzoic acid / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLee, J.H.Z. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP140103229 Australia
CitationJournal: Chemistry / Year: 2022
Title: Selective Oxidations Using a Cytochrome P450 Enzyme Variant Driven with Surrogate Oxygen Donors and Light.
Authors: Lee, J.H.Z. / Podgorski, M.N. / Moir, M. / Gee, A.R. / Bell, S.G.
History
DepositionMay 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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)45,4734
Polymers44,6151
Non-polymers8583
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.082, 51.495, 79.624
Angle α, β, γ (deg.)90.000, 92.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 /


Mass: 44615.438 Da / Num. of mol.: 1 / Mutation: T252E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (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 / Heme B


Mass: 616.487 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4
#3: Chemical ChemComp-M4F / 4-(trifluoromethoxy)benzoic acid


Mass: 206.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H5F3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 280 / 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: 1.96 Å3/Da / Density % sol: 37.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium Acetate, 100 mM Bis-Tris buffer (adjusted with acetic acid to pH 5.0-5.75) and 20-32 % w/v polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.95→43.23 Å / Num. obs: 24354 / % possible obs: 99.6 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.053 / Rrim(I) all: 0.138 / Net I/σ(I): 8.3 / Num. measured all: 165640 / Scaling rejects: 14
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
1.95-26.71.6581107916420.5240.681.7950.995.9
8.94-43.236.50.05118382810.9990.0220.05526.599.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UVB

5uvb


Resolution: 1.95→43.23 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 2001 8.24 %
Rwork0.1881 22291 -
obs0.192 24292 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.88 Å2 / Biso mean: 27.9169 Å2 / Biso min: 21.31 Å2
Refinement stepCycle: final / Resolution: 1.95→43.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 62 280 3365
Biso mean--24.27 29.95 -
Num. residues----393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-20.35411370.33991539167698
2-2.060.30631510.27316351786100
2.06-2.120.29391370.232915321669100
2.12-2.180.29211380.228815931731100
2.18-2.260.2681500.208315901740100
2.26-2.350.26981390.20315711710100
2.35-2.460.24121420.195915921734100
2.46-2.590.24811410.19671589173099
2.59-2.750.26881310.192516161747100
2.75-2.960.24241430.19515811724100
2.96-3.260.23651460.183716041750100
3.26-3.730.22051390.170416091748100
3.73-4.70.19311540.152315971751100
4.7-43.230.19291530.16791643179699

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