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- PDB-4xe3: OleP, the cytochrome P450 epoxidase from Streptomyces antibioticu... -

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Basic information

Entry
Database: PDB / ID: 4xe3
TitleOleP, the cytochrome P450 epoxidase from Streptomyces antibioticus involved in Oleandomycin biosynthesis: functional analysis and crystallographic structure in complex with clotrimazole.
ComponentsCytochrome P-450
KeywordsOXIDOREDUCTASE / P450 / clotrimazole / epoxidase / oleandomycin
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 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1-[(2-CHLOROPHENYL)(DIPHENYL)METHYL]-1H-IMIDAZOLE / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P-450
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsMontemiglio, L.C. / Parisi, G. / Scaglione, A. / Savino, C. / Vallone, B.
Funding support Italy, 1items
OrganizationGrant numberCountry
Istituto Pasteur-Fondazione Cenci Bolognetti Italy
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: Functional analysis and crystallographic structure of clotrimazole bound OleP, a cytochrome P450 epoxidase from Streptomyces antibioticus involved in oleandomycin biosynthesis.
Authors: Montemiglio, L.C. / Parisi, G. / Scaglione, A. / Sciara, G. / Savino, C. / Vallone, B.
History
DepositionDec 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P-450
B: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,90716
Polymers90,0242
Non-polymers2,88314
Water1,02757
1
A: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5509
Polymers45,0121
Non-polymers1,5388
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3587
Polymers45,0121
Non-polymers1,3466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.937, 117.379, 174.664
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-603-

HOH

DetailsMonomer according to gel filtration chromatography

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Components

#1: Protein Cytochrome P-450


Mass: 45012.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Gene: oleP / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q59819
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CL6 / 1-[(2-CHLOROPHENYL)(DIPHENYL)METHYL]-1H-IMIDAZOLE / CLOTRIMAZOLE


Mass: 344.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H17ClN2 / Comment: medication, antifungal*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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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: 3.4 Å3/Da / Density % sol: 63.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6 M Ammonium Sulphate, 0.1 M HEPES Sodium Salt pH 7.5, 2% (w/v) PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 34700 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6.88 % / Biso Wilson estimate: 56.435 Å2 / Rmerge F obs: 0.141 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.102 / Χ2: 0.981 / Net I/σ(I): 17.32 / Num. measured all: 238711
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.65-2.810.8210.862.131125555252970.94195.4
2.81-30.4550.4993.9136016524852250.5499.6
3-3.240.2690.36.7633695490948980.32499.8
3.24-3.550.1540.16111.9331987452345170.17499.9
3.55-3.970.0840.09920.1129841411341080.10699.9
3.97-4.570.0470.0630.4526142364736410.06499.8
4.57-5.590.040.0534.7822414311131090.05499.9
5.59-7.850.0350.04736.5217559243724350.05199.9
7.85-500.0140.02463.269932146314450.02598.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
SCALAdata scaling
MOLREP3.15phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Y46

2y46


Resolution: 2.65→48.76 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.919 / SU B: 12.694 / SU ML: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.52 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2596 1744 5 %RANDOM
Rwork0.2068 32972 --
obs0.2095 34700 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 190.02 Å2 / Biso mean: 58.33 Å2 / Biso min: 24.87 Å2
Baniso -1Baniso -2Baniso -3
1--3.04 Å20 Å20 Å2
2---1.05 Å20 Å2
3---4.09 Å2
Refinement stepCycle: final / Resolution: 2.65→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6142 0 186 57 6385
Biso mean--54.99 43.72 -
Num. residues----788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196487
X-RAY DIFFRACTIONr_bond_other_d0.0020.026141
X-RAY DIFFRACTIONr_angle_refined_deg1.7722.0088876
X-RAY DIFFRACTIONr_angle_other_deg0.895314061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7135790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43422.635296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.312151015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7131571
X-RAY DIFFRACTIONr_chiral_restr0.1970.21001
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217303
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021502
LS refinement shellResolution: 2.65→2.717 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 98 -
Rwork0.385 2182 -
all-2280 -
obs--90.44 %

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