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- PDB-7v44: Crystal structure of Class I P450 monooxygenase (P450tol) from Rh... -

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Basic information

Entry
Database: PDB / ID: 7v44
TitleCrystal structure of Class I P450 monooxygenase (P450tol) from Rhodococcus coprophilus TC-2 in complex with meta-chlorotoluene.
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
1-chloranyl-2-methyl-benzene / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / p450tol monooxygenase
Similarity search - Component
Biological speciesRhodococcus coprophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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)50,3375
Polymers49,4071
Non-polymers9304
Water13,007722
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-28 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.063, 111.063, 80.570
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-1188-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 726 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-C3U / 1-chloranyl-2-methyl-benzene / 1-Chloro-2-methylbenzene


Mass: 126.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7Cl / 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 722 / 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: 2.9 Å3/Da / Density % sol: 57.64 % / Mosaicity: 0.268 °
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: 1.42→25 Å / Num. obs: 107440 / % possible obs: 99.9 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.019 / Rrim(I) all: 0.065 / Χ2: 1.191 / Net I/σ(I): 9.7 / Num. measured all: 1175096
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.42-1.476.60.559106250.8420.2280.6060.53899.7
1.47-1.539.60.423106210.9410.1420.4470.56199.7
1.53-1.610.10.305106510.9680.10.3210.60199.6
1.6-1.6810.70.218106890.9850.070.2290.67299.9
1.68-1.7911.40.16107110.9920.0490.1670.757100
1.79-1.9312.10.116107060.9960.0350.1210.939100
1.93-2.1212.30.088107240.9970.0260.0911.291100
2.12-2.4312.40.074107860.9980.0220.0781.875100
2.43-3.0612.30.056108470.9990.0170.0581.994100
3.06-2511.80.04110800.9990.0120.0411.94999.8

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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: 1.42→24.19 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.841 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.051
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1722 5314 4.9 %RANDOM
Rwork0.1489 ---
obs0.1501 102070 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.59 Å2 / Biso mean: 18.361 Å2 / Biso min: 8.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å2-0 Å2
3----0.32 Å2
Refinement stepCycle: final / Resolution: 1.42→24.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 62 722 4208
Biso mean--16.04 32.9 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0133613
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173334
X-RAY DIFFRACTIONr_angle_refined_deg2.0011.674925
X-RAY DIFFRACTIONr_angle_other_deg1.5741.5937711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9635441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.99521.729214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11315586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7311532
X-RAY DIFFRACTIONr_chiral_restr0.1090.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024116
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02804
LS refinement shellResolution: 1.422→1.459 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 429 -
Rwork0.248 7482 -
all-7911 -
obs--99.76 %

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