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- PDB-3vm4: Cytochrome P450SP alpha (CYP152B1) in complex with (R)-ibuprophen -

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Basic information

Entry
Database: PDB / ID: 3vm4
TitleCytochrome P450SP alpha (CYP152B1) in complex with (R)-ibuprophen
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 / (2R)-2-[4-(2-methylpropyl)phenyl]propanoic acid / Cytochrome P450
Similarity search - Component
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsFujishiro, T. / Shoji, O. / Nagano, S. / Sugimoto, H. / Shiro, Y. / Watanabe, Y.
CitationJournal: Chem Asian J / Year: 2012
Title: Chiral-substrate-assisted stereoselective epoxidation catalyzed by H2O2-dependent cytochrome P450SP alpha
Authors: Fujishiro, T. / Shoji, O. / Kawakami, N. / Watanabe, T. / Sugimoto, H. / Shiro, Y. / Watanabe, Y.
History
DepositionDec 8, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)46,6855
Polymers45,6261
Non-polymers1,0594
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.390, 94.390, 112.863
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: 45625.848 Da / Num. of mol.: 1 / Fragment: Residues 9-415
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-IZP / (2R)-2-[4-(2-methylpropyl)phenyl]propanoic acid / (R)-Ibuprofen


Mass: 206.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18O2
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 3.18 Å3/Da / Density % sol: 61.33 % / Mosaicity: 0.717 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50mM HEPES, 17.5% MPD, 25mM MES, 10% glycerol, 5mM (R)-ibuprophen, 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: 1.94→20 Å / Num. obs: 43560 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 27.626 Å2 / Rmerge(I) obs: 0.048 / Χ2: 1.143 / Net I/σ(I): 19.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.94-2.0110.70.29742870.9161100
2.01-2.0910.70.21743210.961100
2.09-2.1810.60.1643061.0281100
2.18-2.310.60.11843181.1251100
2.3-2.4410.60.09243141.181100
2.44-2.6310.50.07143291.1361100
2.63-2.910.40.05543321.4391100
2.9-3.3110.30.04243801.2751100
3.31-4.1710.20.03444151.2331100
4.17-209.30.03245581.148199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.94 Å19.76 Å
Translation1.94 Å19.76 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AWM

3awm


Resolution: 1.94→19.76 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.1888 / WRfactor Rwork: 0.1626 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8943 / SU B: 5.015 / SU ML: 0.067 / SU R Cruickshank DPI: 0.2013 / SU Rfree: 0.1088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1861 2132 4.9 %RANDOM
Rwork0.1583 ---
obs0.1596 43382 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.35 Å2 / Biso mean: 19.5151 Å2 / Biso min: 4.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å20 Å2
2---0.28 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.94→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 74 274 3568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223441
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.9854699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1575424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.91422.164171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15215529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0471539
X-RAY DIFFRACTIONr_chiral_restr0.0830.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212725
X-RAY DIFFRACTIONr_mcbond_it0.8381.52051
X-RAY DIFFRACTIONr_mcangle_it1.4523285
X-RAY DIFFRACTIONr_scbond_it2.24531390
X-RAY DIFFRACTIONr_scangle_it3.4194.51405
X-RAY DIFFRACTIONr_rigid_bond_restr1.16433441
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 164 -
Rwork0.157 3009 -
all-3173 -
obs--99.62 %
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)
10.8575-0.0432-0.59250.1458-0.15521.35870.0436-0.20340.1-0.03390.02270.00440.0050.0082-0.06630.0075-0.0392-0.00220.223-0.03450.133414.571-39.109-14.689
20.99372.22970.1785-0.0202-0.3247-3.18020.0486-0.06640.0716-0.0556-0.01470.0334-0.0799-0.068-0.03390.0479-0.0277-0.00490.2638-0.0350.180113.582-40.599-19.304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 415
2X-RAY DIFFRACTION2A501

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