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- PDB-7v40: Crystal structure of Class I P450 monooxygenase (P450tol) from Rh... -

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Basic information

Entry
Database: PDB / ID: 7v40
TitleCrystal structure of Class I P450 monooxygenase (P450tol) from Rhodococcus coprophilus TC-2
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 / PHOSPHATE ION / p450tol monooxygenase
Similarity search - Component
Biological speciesRhodococcus coprophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.43 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

Downloads & links

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Assembly

Deposited unit
A: p450tol monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1183
Polymers49,4071
Non-polymers7112
Water13,043724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-29 kcal/mol
Surface area17850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.092, 111.092, 80.815
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-609-

HOH

21A-1158-

HOH

31A-1324-

HOH

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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-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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 724 / 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: 57.79 % / Mosaicity: 0.283 °
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: 1.43→25 Å / Num. obs: 102645 / % possible obs: 97 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.019 / Rrim(I) all: 0.067 / Χ2: 1.097 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.43-1.488.90.68795460.8110.2320.7280.53691
1.48-1.5410.70.52598780.9240.1610.550.55593.9
1.54-1.61110.37298900.960.1130.3890.60594.2
1.61-1.711.50.25599970.9810.0760.2660.6995.1
1.7-1.812.10.182102030.990.0540.190.78896.9
1.8-1.9412.30.131104760.9940.0390.1370.99999.3
1.94-2.1412.50.092105340.9970.0270.0961.2599.5
2.14-2.4412.40.077105610.9980.0230.0811.68899.8
2.44-3.0812.50.056106520.9990.0160.0591.67399.9
3.08-2511.40.043109080.9990.0130.0451.72899.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0232refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CPT

1cpt


Resolution: 1.43→24.25 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.894 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.054
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1749 5079 4.9 %RANDOM
Rwork0.1514 ---
obs0.1525 97551 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.07 Å2 / Biso mean: 20.33 Å2 / Biso min: 10.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å20 Å2
2--0.09 Å2-0 Å2
3----0.3 Å2
Refinement stepCycle: final / Resolution: 1.43→24.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 48 724 4196
Biso mean--15.6 34.12 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0133597
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173317
X-RAY DIFFRACTIONr_angle_refined_deg2.0051.6664906
X-RAY DIFFRACTIONr_angle_other_deg1.5751.5897676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9845441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.69621.84212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9715586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3111531
X-RAY DIFFRACTIONr_chiral_restr0.1090.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024102
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02795
LS refinement shellResolution: 1.431→1.468 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 384 -
Rwork0.246 6544 -
all-6928 -
obs--89.59 %

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