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- PDB-7tnd: The crystal structure of CYP199A4 bound to 4-phenoxybenzoic acid -

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Basic information

Entry
Database: PDB / ID: 7tnd
TitleThe crystal structure of CYP199A4 bound to 4-phenoxybenzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / aromatic / CYP199A4
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-phenoxybenzoic acid / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.825 Å
AuthorsPodgorski, M. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Chemistry / Year: 2022
Title: Enabling Aromatic Hydroxylation in a Cytochrome P450 Monooxygenase Enzyme through Protein Engineering.
Authors: Coleman, T. / Lee, J.Z.H. / Kirk, A.M. / Doherty, D.Z. / Podgorski, M.N. / Pinidiya, D.K. / Bruning, J.B. / De Voss, J.J. / Krenske, E.H. / Bell, S.G.
History
DepositionJan 20, 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

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4544
Polymers44,5871
Non-polymers8663
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-37 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.074, 51.279, 78.953
Angle α, β, γ (deg.)90.000, 92.190, 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 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-JO4 / 4-phenoxybenzoic acid


Mass: 214.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10O3 / 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.: 417 / 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 Å3/Da / Density % sol: 38.49 %
Crystal growTemperature: 289.15 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: 5.00-5.75

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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: Mar 19, 2021
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: 1.82→44.04 Å / Num. obs: 31477 / % possible obs: 98.4 % / Redundancy: 6.7 % / CC1/2: 0.979 / Rmerge(I) obs: 0.339 / Rpim(I) all: 0.141 / Rrim(I) all: 0.368 / Net I/σ(I): 4.5 / Num. measured all: 211509 / Scaling rejects: 103
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
1.82-1.855.52.25800514510.2661.022.4820.677.6
9.08-44.046.20.06917172770.9920.0290.07518.997.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.81 Å43 Å
Translation5.81 Å43 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: 1.825→39.448 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2447 1567 5.01 %
Rwork0.2029 29684 -
obs0.2051 31251 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.61 Å2 / Biso mean: 16.2146 Å2 / Biso min: 4.17 Å2
Refinement stepCycle: final / Resolution: 1.825→39.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 69 417 3507
Biso mean--10.07 23.89 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033188
X-RAY DIFFRACTIONf_angle_d0.5024358
X-RAY DIFFRACTIONf_chiral_restr0.04473
X-RAY DIFFRACTIONf_plane_restr0.003579
X-RAY DIFFRACTIONf_dihedral_angle_d17.3981905
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.825-1.88390.34511350.294255394
1.8839-1.95120.32761370.2852667100
1.9512-2.02940.32971450.26252703100
2.0294-2.12170.28591430.24642706100
2.1217-2.23360.28111430.22712696100
2.2336-2.37350.27051400.20592691100
2.3735-2.55670.23961460.20172713100
2.5567-2.81390.27681410.20762711100
2.8139-3.2210.2431470.18362723100
3.221-4.05740.20311410.1557272999
4.0574-39.4480.15751490.1606279299

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