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- PDB-3wsp: Crystal Structure of P450BM3 with N-perfluorononanoyl-L-tryptophan -

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Basic information

Entry
Database: PDB / ID: 3wsp
TitleCrystal Structure of P450BM3 with N-perfluorononanoyl-L-tryptophan
ComponentsBifunctional P-450/NADPH-P450 reductase
KeywordsOXIDOREDUCTASE / Cytochrome P450
Function / homology
Function and homology information


NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding ...NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / identical protein binding / cytosol
Similarity search - Function
Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Cytochrome p450 / Cytochrome P450 / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. ...Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Cytochrome p450 / Cytochrome P450 / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-W09 / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsCong, Z. / Shoji, O. / Kasai, C. / Sugimoto, H. / Shiro, Y. / Watanabe, Y.
CitationJournal: ACS CATALYSIS / Year: 2015
Title: Activation of Wild-type Cytochrome P450BM3 by the Next Generation of Decoy Molecules: Enhanced Hydroxylation of Gaseous Alkanes and Crystallographic Evidence.
Authors: Cong, Z. / Shoji, O. / Kasai, C. / Kawakami, N. / Sugimoto, H. / Shiro, Y. / Watanabe, Y.
History
DepositionMar 20, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: 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 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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: Bifunctional P-450/NADPH-P450 reductase
B: Bifunctional P-450/NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,2918
Polymers104,6012
Non-polymers2,6906
Water10,016556
1
A: Bifunctional P-450/NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6464
Polymers52,3011
Non-polymers1,3453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bifunctional P-450/NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6464
Polymers52,3011
Non-polymers1,3453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.875, 145.392, 63.029
Angle α, β, γ (deg.)90.000, 97.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bifunctional P-450/NADPH-P450 reductase / Cytochrome P450(BM-3) / Cytochrome P450BM-3 / Cytochrome P450 102 / NADPH--cytochrome P450 reductase


Mass: 52300.660 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Strain: ATCC 14581 / Gene: cyp102, cyp102A1, J04832.1 / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-W09 / N-(2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,9-heptadecafluorononanoyl)-L-tryptophan


Mass: 650.286 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H11F17N2O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.58 Å3/Da / Density % sol: 52.26 % / Mosaicity: 1.238 ° / Mosaicity esd: 0.003 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 75mM Tris-HCl (pH7.9), 50uM N-perfluorononanoyl L-tryptophan, 0.5% (v/v) dimethyl sulfoxide, 105mM MgCl and 10.5% (w/v) PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MAR225 / Detector: CCD / Date: Dec 16, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 91778 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 16.083 Å2 / Rmerge(I) obs: 0.059 / Χ2: 0.985 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.863.10.394540.73298.5
1.86-1.943.10.24293530.9197
1.94-2.033.10.16792490.90895.5
2.03-2.133.20.12790051.05993.8
2.13-2.273.20.10588611.06191.6
2.27-2.443.20.0887241.06390.4
2.44-2.693.20.06788491.03391.3
2.69-3.073.10.06190811.02794
3.07-3.873.10.04994491.04497.7
3.87-203.40.03197531.02299.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation20.04 Å1.95 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREP11.0.05phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZO9

1zo9


Resolution: 1.8→19.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2142 / WRfactor Rwork: 0.175 / FOM work R set: 0.8682 / SU B: 2.434 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1258 / SU Rfree: 0.1212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 4600 5 %RANDOM
Rwork0.1741 ---
obs0.176 91739 94.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.99 Å2 / Biso mean: 22.965 Å2 / Biso min: 9.47 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7310 0 178 556 8044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.027815
X-RAY DIFFRACTIONr_bond_other_d0.0050.027419
X-RAY DIFFRACTIONr_angle_refined_deg1.0991.99510642
X-RAY DIFFRACTIONr_angle_other_deg0.6823.00117134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8135936
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67424.92376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.312151388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4441540
X-RAY DIFFRACTIONr_chiral_restr0.1650.21143
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218779
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021771
LS refinement shellResolution: 1.798→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 315 -
Rwork0.221 6097 -
all-6412 -
obs--90.22 %

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