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- PDB-5b2w: Crystal Structure of P450BM3 with N-perfluorododecanoyl-L-tryptophan -

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Basic information

Entry
Database: PDB / ID: 5b2w
TitleCrystal Structure of P450BM3 with N-perfluorododecanoyl-L-tryptophan
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / Cytochrome P450
Function / homology
Function and homology information


aromatase activity / 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 / 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 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / 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 / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-W1Z / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsCong, Z. / Shoji, O. / Kasai, C. / Sugimoto, H. / Shiro, Y. / Watanabe, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
The Ministry of Education, Culture, Sports, Science, and Technology24225004 Japan
The Ministry of Education, Culture, Sports, Science, and Technology15H05806 Japan
The Japan Science and Technology Agency (JST)15658843 Japan
CitationJournal: to be published
Title: Crystal Structure of P450BM3 with decoy molecules
Authors: Cong, Z. / Shoji, O. / Kasai, C. / Sugimoto, H. / Shiro, Y. / Watanabe, Y.
History
DepositionFeb 3, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional cytochrome P450/NADPH--P450 reductase
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4356
Polymers104,6012
Non-polymers2,8344
Water11,728651
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-42 kcal/mol
Surface area36090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.646, 145.829, 62.771
Angle α, β, γ (deg.)90.000, 97.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 52300.660 Da / Num. of mol.: 2 / Fragment: UNP Residues 4-456 / Mutation: Wild-type
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: cyp102A1, cyp102 / 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-W1Z / (2~{S})-3-(1~{H}-indol-3-yl)-2-[2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,12-tricosakis(fluoranyl)dodecanoylamino]propanoic acid


Mass: 800.308 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H11F23N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 651 / 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: 2.57 Å3/Da / Density % sol: 52.08 % / Mosaicity: 0.764 ° / Mosaicity esd: 0.002 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 75mM Tris-HCl (pH7.9), 50uM N-perfluorododecanoylL-tryptophan, 0.5% (v/v) dimethyl sulfoxide, 105mM MgCl, 10.5% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 27, 2015
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 121491 / % possible obs: 97.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.027 / Rrim(I) all: 0.052 / Χ2: 0.917 / Net I/av σ(I): 27.418 / Net I/σ(I): 11.6 / Num. measured all: 443942
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.65-1.713.70.384195.5
1.71-1.783.70.289195.8
1.78-1.863.70.213196.2
1.86-1.963.70.157196.5
1.96-2.083.70.097196.8
2.08-2.243.70.074197.3
2.24-2.463.70.058197.7
2.46-2.823.70.043198.2
2.82-3.553.60.032198.5
3.55-503.60.021198

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WSP

3wsp


Resolution: 1.65→38.65 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.718 / SU ML: 0.06 / SU R Cruickshank DPI: 0.0992 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.094
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 6109 5 %RANDOM
Rwork0.1854 ---
obs0.1866 115371 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 85.71 Å2 / Biso mean: 22.412 Å2 / Biso min: 10.07 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.65→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7292 0 188 651 8131
Biso mean--25.4 27.55 -
Num. residues----904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197769
X-RAY DIFFRACTIONr_bond_other_d0.0010.027313
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.99810597
X-RAY DIFFRACTIONr_angle_other_deg0.753.00116893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5985928
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28224.881379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.969151367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4151542
X-RAY DIFFRACTIONr_chiral_restr0.1690.21131
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218746
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021764
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 442 -
Rwork0.226 8279 -
all-8721 -
obs--94.43 %

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