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- PDB-3vno: Cytochrome P450SP alpha (CYP152B1) mutant R241E -

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Basic information

Entry
Database: PDB / ID: 3vno
TitleCytochrome P450SP alpha (CYP152B1) mutant R241E
ComponentsFatty acid alpha-hydroxylase
KeywordsOXIDOREDUCTASE / Cytochrome P450
Function / homology
Function and homology information


sterol metabolic process / 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, E-class, group I / Cytochrome p450 / Cytochrome P450 / 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 speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.17 Å
AuthorsFujishiro, T. / Shoji, O. / Sugimoto, H. / Shiro, Y. / Watanabe, Y.
CitationJournal: Catalysis Science And Technology / Year: 2016
Title: A substrate-binding-state mimic of H2O2-dependent cytochrome P450 produced by one-point mutagenesis and peroxygenation of non-native substrates
Authors: Shoji, O. / Fujishiro, T. / Nishio, K. / Kano, Y. / Kimoto, H. / Chien, S.-C. / Onoda, H. / Muramatsu, A. / Tanaka, S. / Hori, A. / Sugimoto, H. / Shiro, Y. / Watanabe, Y.
History
DepositionJan 17, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Fatty acid alpha-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3323
Polymers45,5981
Non-polymers7352
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.539, 94.539, 113.004
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Fatty acid alpha-hydroxylase / Cytochrome P450SP alpha / CYP152B1


Mass: 45597.766 Da / Num. of mol.: 1 / Fragment: Residues 9-415 / Mutation: R241E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Plasmid: pGEX-AX2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O24782, fatty-acid peroxygenase
#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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 3.2 Å3/Da / Density % sol: 61.53 % / Mosaicity: 0.294 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50mM HEPES, 17.5% MPD, 25mM MES, 10% glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Nov 24, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→20 Å / Num. obs: 31376 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 42.762 Å2 / Rmerge(I) obs: 0.048 / Χ2: 1.095 / Net I/σ(I): 19.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.17-2.2510.90.33931061.0651100
2.25-2.3410.90.25830841.071100
2.34-2.4410.90.18330971.1391100
2.44-2.5710.80.14131101.1281100
2.57-2.7310.70.09831121.1081100
2.73-2.9410.70.07131341.2281100
2.94-3.2410.50.05331161.121100
3.24-3.710.40.04231551.0441100
3.7-4.6610.10.03631811.051199.9
4.66-209.10.03432810.984199

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.17 Å19.79 Å
Translation2.17 Å19.79 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AWM

3awm


Resolution: 2.17→19.79 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2373 / WRfactor Rwork: 0.2085 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.856 / SU B: 9.696 / SU ML: 0.115 / SU R Cruickshank DPI: 0.2 / SU Rfree: 0.1687 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 1516 4.9 %RANDOM
Rwork0.1993 ---
obs0.2006 31226 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 104.19 Å2 / Biso mean: 18.1839 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å2-0 Å2
2--0.11 Å2-0 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.17→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3218 0 51 81 3350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223372
X-RAY DIFFRACTIONr_angle_refined_deg1.251.9814594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5395410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23422.275167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82115518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4231537
X-RAY DIFFRACTIONr_chiral_restr0.0840.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212665
X-RAY DIFFRACTIONr_mcbond_it0.6411.52030
X-RAY DIFFRACTIONr_mcangle_it1.17723241
X-RAY DIFFRACTIONr_scbond_it1.70331342
X-RAY DIFFRACTIONr_scangle_it2.6854.51351
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 101 -
Rwork0.221 2139 -
all-2240 -
obs--99.47 %
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)
11.21490.58720.56982.0431.24053.66020.2192-0.2024-0.06950.4778-0.1052-0.30370.04930.0787-0.1140.385-0.0953-0.07790.05580.03540.2812-41.2176.94.078
2-1.1298-1.13691.16533.12081.6109-2.46260.0234-0.0828-0.03620.16750.065-0.22040.13170.0316-0.08840.4743-0.0897-0.06210.19050.05280.4187-41.8968.404-0.699
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 415
2X-RAY DIFFRACTION2A501

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