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- PDB-3aba: Crystal structure of CYP105P1 in complex with filipin I -

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Basic information

Entry
Database: PDB / ID: 3aba
TitleCrystal structure of CYP105P1 in complex with filipin I
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE/ANTIBIOTIC / P450 / oxidoreductase / heme / monooxygenase / macrolide / filipin / Iron / Metal-binding / OXIDOREDUCTASE-ANTIBIOTIC complex
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
Chem-FLI / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsXu, L.H. / Fushinobu, S. / Takamatsu, S. / Wakagi, T. / Ikeda, H. / Shoun, H.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Regio- and stereospecificity of filipin hydroxylation sites revealed by crystal structures of cytochrome P450 105P1 and 105D6 from Streptomyces avermitilis
Authors: Xu, L.H. / Fushinobu, S. / Takamatsu, S. / Wakagi, T. / Ikeda, H. / Shoun, H.
#1: Journal: J.Bacteriol. / Year: 2009
Title: Crystal structures of cytochrome P450 105P1 from Streptomyces avermitilis: conformational flexibility and histidine ligation state
Authors: Xu, L.H. / Fushinobu, S. / Ikeda, H. / Wakagi, T. / Shoun, H.
History
DepositionDec 4, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)45,9576
Polymers44,4291
Non-polymers1,5285
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.368, 91.368, 151.239
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

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Components

#1: Protein Cytochrome P450 / Cytochrome P450 hydroxylase / CYP105P1


Mass: 44429.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Strain: MA-4680 / Gene: pteC, SAV413, SAV_413 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codonplus (DE3)
References: UniProt: Q93H81, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#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-FLI / (3R,4S,6S,8S,10R,12R,14R,16S,17E,19E,21E,23E,25E,28R)-3-hexyl-4,6,8,10,12,14,16-heptahydroxy-17,28-dimethyloxacyclooctacosa-17,19,21,23,25-pentaen-2-one / Filipin I


Mass: 622.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H58O9
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 3.55 Å3/Da / Density % sol: 65.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: (NH4)2SO4, Li2SO4, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 24, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 59975 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 38.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3E5J

3e5j


Resolution: 1.8→39.74 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.688 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23802 2980 5.1 %RANDOM
Rwork0.18754 ---
obs0.19001 55867 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.525 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.2373 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3081 0 102 592 3775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0223253
X-RAY DIFFRACTIONr_angle_refined_deg2.1382.024434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7325396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70523.113151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63315508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0081532
X-RAY DIFFRACTIONr_chiral_restr0.1770.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212495
X-RAY DIFFRACTIONr_mcbond_it1.2491.51979
X-RAY DIFFRACTIONr_mcangle_it2.03523186
X-RAY DIFFRACTIONr_scbond_it3.5731274
X-RAY DIFFRACTIONr_scangle_it5.3074.51248
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 225 -
Rwork0.211 4122 -
obs--99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5062-0.0257-0.03990.57190.04021.0047-0.0479-0.033-0.04940.1229-0.05430.11220.0737-0.20060.10210.0508-0.040.06240.1067-0.03840.0934-7.78233.826.46
20.2256-0.3272-0.05810.52980.08460.2582-0.01760.00320.0118-0.0334-0.02440.0081-0.0239-0.00840.04190.0754-0.0019-0.01620.0832-0.0140.072211.5445.19911.419
30.0812-0.0119-0.05330.24060.09430.3367-0.02650.02060.00010.0348-0.02310.0449-0.0088-0.03480.04950.0728-0.00870.00940.0888-0.02250.06826.06443.03717.818
40.4303-0.1616-0.27970.26170.19390.2756-0.0390.0306-0.02550.0352-0.04980.04930.062-0.02050.08870.0866-0.01050.0130.0867-0.01620.073410.42229.4211.88
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 82
2X-RAY DIFFRACTION2A83 - 146
3X-RAY DIFFRACTION3A147 - 323
4X-RAY DIFFRACTION4A324 - 403

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