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- PDB-3vtj: Cytochrome P450SP alpha (CYP152B1) mutant A245H -

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Basic information

Entry
Database: PDB / ID: 3vtj
TitleCytochrome P450SP alpha (CYP152B1) mutant A245H
ComponentsFatty acid alpha-hydroxylase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Peroxygenase
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: 2.56 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
DepositionMay 30, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 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)47,2342
Polymers46,6171
Non-polymers6161
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.558, 94.558, 114.183
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Fatty acid alpha-hydroxylase


Mass: 46617.047 Da / Num. of mol.: 1 / Mutation: A245H
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.16 Å3/Da / Density % sol: 61.09 % / Mosaicity: 0.309 °
Crystal growTemperature: 277 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 277K

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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: Jan 27, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. obs: 19489 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 48.68 Å2 / Rmerge(I) obs: 0.11 / Χ2: 1.023 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.56-2.6510.80.3518980.8411100
2.65-2.7610.70.28919090.8781100
2.76-2.8810.80.22119031.0041100
2.88-3.0410.70.17519531.1141100
3.04-3.2310.70.13819211.0931100
3.23-3.4710.60.11419331.0741100
3.47-3.8210.50.10219571.1151100
3.82-4.3810.40.09319460.9941100
4.38-5.5110.10.08519931.0261100
5.51-509.10.0920761.095199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.72 Å38.54 Å
Translation2.72 Å38.54 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AWM

3awm


Resolution: 2.56→19.94 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.2384 / WRfactor Rwork: 0.1902 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8556 / SU B: 15.841 / SU ML: 0.173 / SU R Cruickshank DPI: 0.3995 / SU Rfree: 0.2607 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.399 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 991 5.1 %RANDOM
Rwork0.1881 ---
obs0.1904 18363 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.31 Å2 / Biso mean: 43.158 Å2 / Biso min: 7.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.04 Å20 Å2
2---0.09 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.56→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 43 56 3324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193371
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.9544590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9485408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.53122.083168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69415518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6041538
X-RAY DIFFRACTIONr_chiral_restr0.070.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212672
LS refinement shellResolution: 2.561→2.627 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 61 -
Rwork0.257 1238 -
all-1299 -
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)
11.0118-0.36840.34861.0475-0.56792.55710.12430.1049-0.0375-0.1955-0.06410.1353-0.0541-0.0374-0.06010.20350.0624-0.04160.0249-0.01080.124741.2967.04915.124
22.27843.14951.02485.54281.55680.4775-0.18620.02220.4894-0.26530.05110.1453-0.08220.01260.13520.38950.0664-0.05070.07730.01120.360842.1698.71819.85
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 410
2X-RAY DIFFRACTION2A501

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