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- PDB-1izo: Cytochrome P450 BS beta Complexed with Fatty Acid -

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Basic information

Entry
Database: PDB / ID: 1izo
TitleCytochrome P450 BS beta Complexed with Fatty Acid
ComponentsCytochrome P450 152A1
KeywordsOXIDOREDUCTASE / HEME PROTEIN / PROTEIN-FATTY ACID COMPLEX / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


fatty-acid peroxygenase / 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 / PALMITOLEIC ACID / Fatty-acid peroxygenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsLee, D.S. / Yamada, A. / Sugimoto, H. / Matsunaga, I. / Ogura, H. / Ichihara, K. / Adachi, S. / Park, S.Y. / Shiro, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Substrate Recognition and Molecular Mechanism of Fatty Acid Hydroxylation by Cytochrome P450 from Bacillus subtilis. CRYSTALLOGRAPHIC, SPECTROSCOPIC, AND MUTATIONAL STUDIES.
Authors: Lee, D.S. / Yamada, A. / Sugimoto, H. / Matsunaga, I. / Ogura, H. / Ichihara, K. / Adachi, S. / Park, S.Y. / Shiro, Y.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization and preliminary X-ray diffraction analysis of fatty-acid hydroxylase cytochrome P450BSbeta from Bacillus subtilis.
Authors: Lee, D.S. / Yamada, A. / Matsunaga, I. / Ichihara, K. / Adachi, S. / Park, S.Y. / Shiro, Y.
History
DepositionOct 10, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: Cytochrome P450 152A1
B: Cytochrome P450 152A1
C: Cytochrome P450 152A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,1569
Polymers144,5433
Non-polymers2,6136
Water5,314295
1
A: Cytochrome P450 152A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0523
Polymers48,1811
Non-polymers8712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 152A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0523
Polymers48,1811
Non-polymers8712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450 152A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0523
Polymers48,1811
Non-polymers8712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.789, 155.789, 111.904
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThis Enzyme Exists As A Monomer.

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Components

#1: Protein Cytochrome P450 152A1 / P450BsBeta


Mass: 48181.066 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: O31440, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H30O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.67 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 10%(w/v) PEG 3350, 50 mM MES, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
210 %(w/v)PEG33501reservoir
350 mMMES1reservoirpH6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 90731 / Num. obs: 87103 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.326 / Net I/σ(I): 16.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 1 / Num. unique all: 7032 / % possible all: 81.5
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 7.4 % / Num. measured all: 618052 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 81.5 % / Mean I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→20 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 4410 5 %RANDOM
Rwork0.246 ---
all-91204 --
obs-87409 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.1666 Å2 / ksol: 0.362316 e/Å3
Displacement parametersBiso mean: 52.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å22.87 Å20 Å2
2--1.46 Å20 Å2
3----2.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10017 0 183 295 10495
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 676 5.1 %
Rwork0.326 12702 -
obs--88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3HEM.PARAMHEM.TOP
X-RAY DIFFRACTION4PAM.PARAMPAM.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
LS refinement shell
*PLUS
Lowest resolution: 2.18 Å

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