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- PDB-3e5j: Crystal structure of CYP105P1 wild-type ligand-free form -

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Basic information

Entry
Database: PDB / ID: 3e5j
TitleCrystal structure of CYP105P1 wild-type ligand-free form
ComponentsCytochrome P450 (Cytochrome P450 hydroxylase)
KeywordsOXIDOREDUCTASE / P450 / Heme / Iron / Metal-binding / Monooxygenase
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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsXu, L.H. / Fushinobu, S. / Ikeda, H. / Wakagi, T. / Shoun, H.
CitationJournal: 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
DepositionAug 14, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Nov 1, 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: Cytochrome P450 (Cytochrome P450 hydroxylase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0282
Polymers44,4111
Non-polymers6161
Water8,773487
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cytochrome P450 (Cytochrome P450 hydroxylase)
hetero molecules

A: Cytochrome P450 (Cytochrome P450 hydroxylase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0564
Polymers88,8232
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3690 Å2
ΔGint-68.9 kcal/mol
Surface area32280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.401, 88.401, 193.885
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 44411.457 Da / Num. of mol.: 1 / Mutation: M387I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Strain: MA-4680 / Gene: pteC, SAV413, SAV_413 / Plasmid: pET-17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus (DE3) / References: UniProt: Q93H81
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 4.26 Å3/Da / Density % sol: 71.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 3.7M sodium formate, pH8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 26, 2007
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 57002 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 34.735 Å2 / Rsym value: 0.051 / Net I/σ(I): 65.3
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 14.1 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.409 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BVJ

2bvj


Resolution: 1.95→38.75 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.318 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21065 2874 5.1 %RANDOM
Rwork0.18965 ---
obs0.19072 53921 99.84 %-
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: 32.769 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.107 Å0.113 Å
Refinement stepCycle: LAST / Resolution: 1.95→38.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3019 0 43 487 3549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223130
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6042.014269
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0785388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93123.129147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.36315497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7161532
X-RAY DIFFRACTIONr_chiral_restr0.1210.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022420
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.21658
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22175
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2433
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3070.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0161.52003
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53723124
X-RAY DIFFRACTIONr_scbond_it2.47231255
X-RAY DIFFRACTIONr_scangle_it3.7844.51144
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 202 -
Rwork0.206 3932 -
obs--100 %
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)
12.82050.8665-0.40971.394-0.17711.5222-0.01110.1175-0.1784-0.08270.0753-0.08380.05380.2456-0.0642-0.04970.0469-0.00080.1336-0.0430.081510.405618.788323.8128
21.41010.10260.26571.6394-0.48953.7015-0.02020.2572-0.2108-0.0667-0.1317-0.02120.2658-0.11430.15190.00260.01490.02470.1421-0.06380.0937-13.30377.021915.57
339.1507-44.6297-8.643652.594914.510314.52131.5688-2.28031.0398-1.8807-0.1808-1.26230.05370.1579-1.3880.32430.0028-0.00520.31450.00090.32121.2207-4.15713.7202
41.0896-0.2637-0.2210.69670.1832.9722-0.01170.3085-0.1112-0.1422-0.11120.0330.207-0.08630.12290.03820.01190.01290.1381-0.03780.0965-10.78598.50114.3592
52.51251.245-1.03871.0946-0.69721.77830.0180.01960.14420.05610.0710.0263-0.08980.0957-0.089-0.00780.0370.00390.1056-0.02520.07793.309222.191427.7553
61.44070.17780.18281.48110.25011.935-0.0135-0.1602-0.30810.0873-0.0811-0.14460.4845-0.01050.09450.00560.03410.03520.05550.01830.062-6.69184.249730.0698
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 787 - 78
2X-RAY DIFFRACTION2AA83 - 16883 - 168
3X-RAY DIFFRACTION3AA169 - 180169 - 180
4X-RAY DIFFRACTION4AA181 - 271181 - 271
5X-RAY DIFFRACTION5AA272 - 343272 - 343
6X-RAY DIFFRACTION6AA344 - 400344 - 400

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