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- PDB-3awq: Cytochrome P450SP alpha (CYP152B1) mutant L78F -

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Basic information

Entry
Database: PDB / ID: 3awq
TitleCytochrome P450SP alpha (CYP152B1) mutant L78F
ComponentsFatty acid alpha-hydroxylase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Peroxygenase
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, 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 / PALMITIC ACID / Cytochrome P450
Similarity search - Component
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsFujishiro, T. / Shoji, O. / Nagano, S. / Sugimoto, H. / Shiro, Y. / Watanabe, Y.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal structure of H2O2-dependent cytochrome P450SPalpha with its bound fatty acid substrate: insight into the regioselective hydroxylation of fatty acids at the alpha position.
Authors: Fujishiro, T. / Shoji, O. / Nagano, S. / Sugimoto, H. / Shiro, Y. / Watanabe, Y.
History
DepositionMar 25, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 5, 2013Group: Database references
Revision 1.3Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

Deposited unit
A: Fatty acid alpha-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4573
Polymers46,5841
Non-polymers8732
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.137, 94.137, 113.402
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: 46583.996 Da / Num. of mol.: 1 / Mutation: L78F
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-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 3.11 Å3/Da / Density % sol: 60.5 % / Mosaicity: 0.275 °
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: Jul 23, 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: 1.9→20 Å / Num. obs: 46225 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.075 / Χ2: 1.032 / Net I/σ(I): 16.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.97110.3845880.8271100
1.97-2.05110.27745590.9111100
2.05-2.1410.90.2455811100
2.14-2.2510.90.14745621.0561100
2.25-2.3910.90.11845911.0391100
2.39-2.5810.80.09846161.041100
2.58-2.8410.80.08146071.0861100
2.84-3.2510.70.07146231.0331100
3.25-4.0810.50.06346891.1481100
4.08-209.60.06148321.194199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AWM

3awm


Resolution: 1.9→19.98 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.735 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1877 2266 4.9 %RANDOM
Rwork0.1585 ---
obs0.16 46107 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.36 Å2 / Biso mean: 16.6246 Å2 / Biso min: 2.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3223 0 61 247 3531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223426
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.9844658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4245416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89522.118170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17315524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6911539
X-RAY DIFFRACTIONr_chiral_restr0.0910.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212702
X-RAY DIFFRACTIONr_mcbond_it1.0311.52039
X-RAY DIFFRACTIONr_mcangle_it1.74223260
X-RAY DIFFRACTIONr_scbond_it2.58131387
X-RAY DIFFRACTIONr_scangle_it3.8914.51393
X-RAY DIFFRACTIONr_rigid_bond_restr1.36933426
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 141 -
Rwork0.183 3170 -
all-3311 -
obs--99.22 %
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)
10.4816-0.28530.31520.8991-0.75371.90580.10380.0246-0.0288-0.1882-0.05410.1151-0.03180.0112-0.04970.25030.0729-0.03930.0623-0.02220.164941.2316.96115.143
20.3765-0.5051-0.01362.25080.4748-0.1930.0684-0.0946-0.0148-0.1778-0.04070.0076-0.0483-0.0691-0.02770.31680.0905-0.03060.1164-0.00240.209141.8988.51919.499
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 410
2X-RAY DIFFRACTION2A501

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