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- PDB-3e5l: Crystal structure of CYP105P1 H72A mutant -

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Basic information

Entry
Database: PDB / ID: 3e5l
TitleCrystal structure of CYP105P1 H72A mutant
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: 2.4 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)44,9792
Polymers44,3621
Non-polymers6161
Water4,053225
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)89,9584
Polymers88,7252
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3500 Å2
ΔGint-64.6 kcal/mol
Surface area33380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.635, 88.635, 191.473
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: 44362.426 Da / Num. of mol.: 1 / Mutation: H72A
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.: 225 / 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: 4.24 Å3/Da / Density % sol: 70.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 4.2M 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: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 31, 2008
RadiationMonochromator: Triangular Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 30777 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Biso Wilson estimate: 53.116 Å2 / Rsym value: 0.06 / Net I/σ(I): 48.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.472 / % 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 3E5J

3e5j


Resolution: 2.4→40.23 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.357 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23533 1539 5 %RANDOM
Rwork0.18401 ---
obs0.18656 29066 99.74 %-
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: 41.172 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.194 Å0.206 Å
Refinement stepCycle: LAST / Resolution: 2.4→40.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 43 225 3314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223158
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1862.0114308
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6925393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75523.197147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.0315504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4441532
X-RAY DIFFRACTIONr_chiral_restr0.1510.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022442
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.21590
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22144
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2238
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2621.52023
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.99423161
X-RAY DIFFRACTIONr_scbond_it3.31731268
X-RAY DIFFRACTIONr_scangle_it5.2334.51145
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 110 -
Rwork0.225 2105 -
obs--99.46 %
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)
16.57563.1787-1.24144.1816-2.23022.672-0.11490.17-0.4508-0.5149-0.0212-0.50721.00030.41170.13610.3010.12370.0119-0.1073-0.02630.0044-15.5997-13.6897-32.2202
20.10040.46850.05293.81211.9954.13010.117-0.2117-0.09690.51080.1831-0.40020.41950.3132-0.30010.12160.0028-0.0399-0.04280.01290.0912-20.1367-10.15-15.1953
31.23170.05370.11951.9555-0.00813.3245-0.0740.0040.15810.1812-0.0686-0.1829-0.23910.35250.14260.11430.0064-0.0661-0.00590.02640.0853-6.020214.1341-16.2268
43.8966-4.6719-0.288911.65650.04692.5410.07690.3103-0.0254-0.2752-0.2587-0.24290.1430.52350.18180.1292-0.0261-0.10370.19690.09120.01940.56133.2961-5.9433
50.8585-0.034-0.01681.34950.11043.6796-0.0435-0.11320.05620.2053-0.0129-0.03430.0640.11530.05640.11580.0357-0.00830.0386-0.0040.1459-11.87139.2863-19.6844
61.68660.9392-0.75112.3432-1.01661.72820.08210.02510.00730.00340.00460.13750.1784-0.165-0.08660.14070.0087-0.041400.00260.1079-24.3792-4.8116-26.009
73.3053-0.123-0.70711.70350.14753.1667-0.08290.2153-0.2641-0.1968-0.0566-0.2940.24490.52120.13950.09110.05760.00230.03270.01190.0673-3.79066.5931-30.1372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 337 - 33
2X-RAY DIFFRACTION2AA34 - 9134 - 91
3X-RAY DIFFRACTION3AA92 - 17192 - 171
4X-RAY DIFFRACTION4AA172 - 199172 - 199
5X-RAY DIFFRACTION5AA200 - 288200 - 288
6X-RAY DIFFRACTION6AA289 - 346289 - 346
7X-RAY DIFFRACTION7AA347 - 400347 - 400

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