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- PDB-2zqj: Substrate-Free Form of Cytochrome P450BSbeta -

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Basic information

Entry
Database: PDB / ID: 2zqj
TitleSubstrate-Free Form of Cytochrome P450BSbeta
ComponentsCytochrome P450 152A1
KeywordsOXIDOREDUCTASE / Peroxigenese / Heme protein / Substrate-free form / Heme / Iron / Metal-binding / Monooxygenase
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 / Fatty-acid peroxygenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsShoji, O. / Fujishiro, T. / Nagano, S. / Hirose, T. / Shiro, Y. / Watanabe, Y.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2010
Title: Understanding substrate misrecognition of hydrogen peroxide dependent cytochrome P450 from Bacillus subtilis.
Authors: Shoji, O. / Fujishiro, T. / Nagano, S. / Tanaka, S. / Hirose, T. / Shiro, Y. / Watanabe, Y.
History
DepositionAug 11, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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 / 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: Cytochrome P450 152A1
B: Cytochrome P450 152A1
C: Cytochrome P450 152A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,3936
Polymers144,5433
Non-polymers1,8493
Water1,02757
1
A: Cytochrome P450 152A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7982
Polymers48,1811
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 152A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7982
Polymers48,1811
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome P450 152A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7982
Polymers48,1811
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)173.076, 173.076, 279.616
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Cytochrome P450 152A1 / P450BsBeta / Fatty acid beta-hydroxylase


Mass: 48181.066 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: cypC, CYP152A1, BSU02100 / Plasmid: pQE30 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 12.5%(w/v) PEG3350, 50mM Tris-HCl, 0.1M MgCl2, 20% glycerol, pH8.1, 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: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 34186 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 71.4 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 28.32

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IZO

1izo


Resolution: 2.9→46.6 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1708 -RANDOM
Rwork0.221 ---
obs0.221 34185 95 %-
Displacement parametersBiso mean: 47 Å2
Baniso -1Baniso -2Baniso -3
1--8.4 Å213.7 Å20 Å2
2---8.4 Å20 Å2
3---16.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.9→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10017 0 129 57 10203
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d1.06
LS refinement shellResolution: 2.37→2.52 Å / Rfactor Rwork: 0.286

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