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- PDB-7v41: Crystal structure of Class I P450 monooxygenase (P450tol) from Rh... -

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Basic information

Entry
Database: PDB / ID: 7v41
TitleCrystal structure of Class I P450 monooxygenase (P450tol) from Rhodococcus coprophilus TC-2 in complex with toluene.
Componentsp450tol monooxygenase
KeywordsELECTRON TRANSPORT / HEM
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 / TOLUENE / PHOSPHATE ION / p450tol monooxygenase
Similarity search - Component
Biological speciesRhodococcus coprophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsZhang, L.L. / Huang, J.W. / Liu, W.D. / Chen, C.C. / Guo, R.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2022
Title: Molecular Basis for a Toluene Monooxygenase to Govern Substrate Selectivity
Authors: Chen, C.C. / Dai, M. / Zhang, L. / Zhao, J. / Zeng, W. / Shi, M. / Huang, J.W. / Liu, W. / Guo, R.T. / Li, A.
History
DepositionAug 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: p450tol monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2104
Polymers49,4071
Non-polymers8043
Water13,511750
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-28 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.164, 111.164, 80.576
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein p450tol monooxygenase


Mass: 49406.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus coprophilus (bacteria) / Plasmid: pRSF-Duet I / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A088FL33
#2: Chemical ChemComp-MBN / TOLUENE


Mass: 92.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8
#3: 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
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 750 / 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: 2.91 Å3/Da / Density % sol: 57.72 % / Mosaicity: 0.378 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: Na/K phosphate, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 10, 2019
RadiationMonochromator: LN2 cooled Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.45→25 Å / Num. obs: 97020 / % possible obs: 95.4 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.017 / Rrim(I) all: 0.061 / Χ2: 1.279 / Net I/σ(I): 12.2 / Num. measured all: 1095791
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.58.60.33686520.9550.1160.3570.56586
1.5-1.569.40.2694950.9760.0860.2750.59394.1
1.56-1.639.90.19695640.9860.0630.2060.6594.5
1.63-1.7210.70.14895740.9920.0470.1560.74794.9
1.72-1.8311.50.11596320.9960.0350.1210.86995.5
1.83-1.9712.20.09198110.9970.0270.0951.06296.8
1.97-2.1712.60.07198920.9980.0210.0741.43697.3
2.17-2.4812.70.06199590.9990.0180.0631.76697.9
2.48-3.1212.70.051100880.9990.0150.0532.00798.4
3.12-2512.20.042103530.9990.0130.0442.21198.6

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CPT

1cpt


Resolution: 1.45→24.08 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.783 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.055
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1704 4911 5.1 %RANDOM
Rwork0.1473 ---
obs0.1485 92109 95.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.46 Å2 / Biso mean: 16.26 Å2 / Biso min: 6.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å2-0 Å2
2--0.14 Å20 Å2
3----0.44 Å2
Refinement stepCycle: final / Resolution: 1.45→24.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 0 55 752 4224
Biso mean--11.65 30.5 -
Num. residues----431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0133597
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173314
X-RAY DIFFRACTIONr_angle_refined_deg2.0481.6684905
X-RAY DIFFRACTIONr_angle_other_deg1.5871.5937667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0795440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.11121.878213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62515583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3441531
X-RAY DIFFRACTIONr_chiral_restr0.1110.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024106
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02799
LS refinement shellResolution: 1.45→1.487 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.207 277 -
Rwork0.194 5807 -
obs--81.86 %

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