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- PDB-7tp5: The crystal structure of T252E CYP199A4 bound to 4-ethylthiobenzo... -

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Basic information

Entry
Database: PDB / ID: 7tp5
TitleThe crystal structure of T252E CYP199A4 bound to 4-ethylthiobenzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / peroxygenase / sulfoxidation
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-(ethylsulfanyl)benzoic acid / ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.655 Å
AuthorsPodgorski, M. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Chemistry / Year: 2022
Title: Investigating the Active Oxidants Involved in Cytochrome P450 Catalyzed Sulfoxidation Reactions.
Authors: Podgorski, M.N. / Coleman, T. / Churchman, L.R. / Bruning, J.B. / De Voss, J.J. / Bell, S.G.
History
DepositionJan 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5927
Polymers44,6151
Non-polymers9776
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-41 kcal/mol
Surface area15110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.730, 51.500, 79.280
Angle α, β, γ (deg.)90.000, 92.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome P450


Mass: 44615.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris HaA2 (phototrophic)
Strain: HaA2 / Gene: RPB_3613 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2IU02

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Non-polymers , 6 types, 401 molecules

#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-81M / 4-(ethylsulfanyl)benzoic acid


Mass: 182.239 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O2S / 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.87 Å3/Da / Density % sol: 34.23 %
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: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 5, 2018
RadiationMonochromator: Double-crystal Si(111) water-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.655→40.7 Å / Num. obs: 31873 / % possible obs: 81.1 % / Redundancy: 5 % / Biso Wilson estimate: 13.11 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.067 / Rrim(I) all: 0.161 / Net I/σ(I): 9.3
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
1.66-1.684.31.521616714220.3760.7631.712173.3
9.06-40.750.04112682530.9980.0190.04632.296

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.68 Å40.7 Å
Translation5.68 Å40.7 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.6.3data 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: 1.655→40.697 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2039 1629 5.11 %
Rwork0.1668 30236 -
obs0.1687 31865 81.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.18 Å2 / Biso mean: 16.5554 Å2 / Biso min: 5.42 Å2
Refinement stepCycle: final / Resolution: 1.655→40.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 65 395 3483
Biso mean--12.24 24.76 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043202
X-RAY DIFFRACTIONf_angle_d0.7324373
X-RAY DIFFRACTIONf_chiral_restr0.046472
X-RAY DIFFRACTIONf_plane_restr0.004584
X-RAY DIFFRACTIONf_dihedral_angle_d8.1583332
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.655-1.70370.31251150.2818227674
1.7037-1.75870.28831190.2648233976
1.7587-1.82160.27611170.2278233075
1.8216-1.89450.25741370.2109232175
1.8945-1.98070.25361340.1926228774
1.9807-2.08510.2061190.1789231975
2.0851-2.21580.21051160.1679232575
2.2158-2.38680.19461180.1611235976
2.3868-2.6270.19671600.1621260184
2.627-3.0070.20981710.1593291794
3.007-3.78810.16811680.138303197
3.7881-40.6970.16831550.1399313197

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