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- PDB-7reh: Crystal structure of T252E CYP199A4 bound to 4-methoxybenzoic acid -

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Basic information

Entry
Database: PDB / ID: 7reh
TitleCrystal structure of T252E CYP199A4 bound to 4-methoxybenzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / peroxygenase / mutant
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 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.545 Å
AuthorsPodgorski, M.N. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Acs Catalysis / Year: 2022
Title: An Altered Heme Environment in an Engineered Cytochrome P450 Enzyme Enables the Switch from Monooxygenase to Peroxygenase Activity
Authors: Podgorski, M.N. / Harbort, J.S. / Lee, J.H.Z. / Nguyen, G.T. / Bruning, J.B. / Donald, W.A. / Bernhardt, P.V. / Harmer, J.R. / Bell, S.G.
History
DepositionJul 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 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)45,6218
Polymers44,6151
Non-polymers1,0067
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-36 kcal/mol
Surface area15190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.310, 51.510, 79.650
Angle α, β, γ (deg.)90.000, 92.210, 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 / Mutation: T252E
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, Oxidoreductases

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Non-polymers , 6 types, 477 molecules

#2: 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
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 1.91 Å3/Da / Density % sol: 35.47 %
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: MX1 / Wavelength: 0.7108 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 8, 2017
RadiationMonochromator: Double-crystal Si(111) water-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7108 Å / Relative weight: 1
ReflectionResolution: 1.545→43.24 Å / Num. obs: 48517 / % possible obs: 98.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 9.15 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.066 / Rrim(I) all: 0.179 / Net I/σ(I): 8.5
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
1.55-1.576.60.9511478022480.7640.3961.0322.292.5
8.46-43.245.90.09918183080.9870.0430.10818.295.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.69 Å29.22 Å
Translation5.69 Å29.22 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.6.2data scaling
PHASER2.7.17phasing
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UVB

5uvb


Resolution: 1.545→29.218 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2031 2430 5.02 %
Rwork0.1707 46008 -
obs0.1723 48438 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.19 Å2 / Biso mean: 12.5518 Å2 / Biso min: 1.52 Å2
Refinement stepCycle: final / Resolution: 1.545→29.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 68 470 3561
Biso mean--9.01 22.85 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073247
X-RAY DIFFRACTIONf_angle_d0.8914438
X-RAY DIFFRACTIONf_chiral_restr0.052477
X-RAY DIFFRACTIONf_plane_restr0.006595
X-RAY DIFFRACTIONf_dihedral_angle_d8.3043347
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.545-1.57650.26841300.2385253393
1.5765-1.61080.28311520.2178268899
1.6108-1.64830.23561190.1971272899
1.6483-1.68950.25711300.1916268599
1.6895-1.73520.22671620.1884269699
1.7352-1.78620.24471510.1818270299
1.7862-1.84390.20781390.1779267899
1.8439-1.90980.21581580.1722270599
1.9098-1.98620.22371360.1701271399
1.9862-2.07660.19741380.1575273199
2.0766-2.1860.17731490.1615269199
2.186-2.32290.19411580.1562271599
2.3229-2.50220.20771530.1683271099
2.5022-2.75380.20951510.1779276299
2.7538-3.15190.18221150.1718275299
3.1519-3.96950.16261260.1488275899
3.9695-29.2180.18571630.1611276198

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