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- PDB-8hgc: Crystal structure of the CYP199A4 mutant F182T in complex with 4-... -

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Basic information

Entry
Database: PDB / ID: 8hgc
TitleCrystal structure of the CYP199A4 mutant F182T in complex with 4-methoxybenzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / CYP199A4 / Complex
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
ACETATE ION / 4-METHOXYBENZOIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsJiang, Y. / Cong, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21977104 China
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Enabling Peroxygenase Activity in Cytochrome P450 Monooxygenases by Engineering Hydrogen Peroxide Tunnels.
Authors: Zhao, P. / Kong, F. / Jiang, Y. / Qin, X. / Tian, X. / Cong, Z.
History
DepositionNov 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

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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)46,8397
Polymers45,8011
Non-polymers1,0386
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-23 kcal/mol
Surface area15070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.326, 51.672, 79.158
Angle α, β, γ (deg.)90.00, 92.55, 90.00
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: 45800.750 Da / Num. of mol.: 1 / Mutation: F182T
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 , 5 types, 435 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ANN / 4-METHOXYBENZOIC ACID / P-ANISIC ACID


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 1.98 Å3/Da / Density % sol: 37.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2 M MgAc, 0.1 M Bis-tris 5.5, 27% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.72→44.28 Å / Num. obs: 34700 / % possible obs: 90.6 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.042 / Rrim(I) all: 0.078 / Χ2: 0.45 / Net I/σ(I): 9.3 / Num. measured all: 116855
Reflection shellResolution: 1.72→1.81 Å / % possible obs: 99.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.496 / Num. measured all: 18867 / Num. unique obs: 5507 / CC1/2: 0.82 / Rpim(I) all: 0.314 / Rrim(I) all: 0.589 / Χ2: 0.43 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
Aimlessdata scaling
XDSdata reduction
PHENIX1.18.2phasing
PDB_EXTRACT4data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PQD

6pqd


Resolution: 1.72→44.28 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.177 3501 10.09 %
Rwork0.1562 --
obs0.1583 34681 90.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.72→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3000 0 72 429 3501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073165
X-RAY DIFFRACTIONf_angle_d0.7434323
X-RAY DIFFRACTIONf_dihedral_angle_d23.3491158
X-RAY DIFFRACTIONf_chiral_restr0.048471
X-RAY DIFFRACTIONf_plane_restr0.005575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.740.26221590.22831335X-RAY DIFFRACTION99
1.74-1.770.24881420.211371X-RAY DIFFRACTION99
1.77-1.790.2181630.19311344X-RAY DIFFRACTION99
1.79-1.820.21671490.19551334X-RAY DIFFRACTION99
1.82-1.850.24151440.18021420X-RAY DIFFRACTION99
1.85-1.870.24221080.1884901X-RAY DIFFRACTION94
1.95-1.990.18441500.17661368X-RAY DIFFRACTION99
1.99-2.040.20821590.17831349X-RAY DIFFRACTION99
2.04-2.080.17721490.16171396X-RAY DIFFRACTION100
2.09-2.140.20241490.16131355X-RAY DIFFRACTION100
2.14-2.190.18991550.16141379X-RAY DIFFRACTION99
2.19-2.260.18431630.16041340X-RAY DIFFRACTION100
2.26-2.330.20981470.15361395X-RAY DIFFRACTION100
2.33-2.420.21151470.16081343X-RAY DIFFRACTION99
2.42-2.510.17271560.15981366X-RAY DIFFRACTION99
2.51-2.630.18581610.16021380X-RAY DIFFRACTION99
2.63-2.770.19371540.16211367X-RAY DIFFRACTION99
2.77-2.940.16811490.1551377X-RAY DIFFRACTION100
2.94-3.170.17771500.15951376X-RAY DIFFRACTION100
3.17-3.480.171580.14611369X-RAY DIFFRACTION100
3.48-3.990.12681600.1231386X-RAY DIFFRACTION99
3.99-5.020.12931460.12691358X-RAY DIFFRACTION98
5.02-44.280.16131620.15971406X-RAY DIFFRACTION97

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