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- PDB-5xa3: Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-prolyl-L-ph... -

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Basic information

Entry
Database: PDB / ID: 5xa3
TitleCrystal Structure of P450BM3 with Benzyloxycarbonyl-L-prolyl-L-phenylalanine
ComponentsBifunctional cytochrome P450/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 / FMN binding / iron ion binding / heme binding / identical protein binding / cytoplasm
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 / PHENYLALANINE / benzyl chlorocarbonate / PROLINE / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsShoji, O. / Yanagisawa, S. / Stanfield, J.K. / Suzuki, K. / Kasai, C. / Cong, Z. / Sugimoto, H. / Shiro, Y. / Watanabe, Y.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Direct Hydroxylation of Benzene to Phenol by Cytochrome P450BM3 Triggered by Amino Acid Derivatives.
Authors: Shoji, O. / Yanagisawa, S. / Stanfield, J.K. / Suzuki, K. / Cong, Z. / Sugimoto, H. / Shiro, Y. / Watanabe, Y.
History
DepositionMar 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)213,78524
Polymers209,2034
Non-polymers4,58220
Water11,476637
1
A: Bifunctional cytochrome P450/NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4466
Polymers52,3011
Non-polymers1,1465
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional cytochrome P450/NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4466
Polymers52,3011
Non-polymers1,1465
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bifunctional cytochrome P450/NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4466
Polymers52,3011
Non-polymers1,1465
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bifunctional cytochrome P450/NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4466
Polymers52,3011
Non-polymers1,1465
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.234, 58.522, 145.952
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Bifunctional cytochrome P450/NADPH-P450 reductase / Cytochrome P450(BM-3) / Cytochrome P450BM-3 / Fatty acid monooxygenase / Flavocytochrome P450 BM3


Mass: 52300.660 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 1-456
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (strain ATCC 14581 / DSM 32 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / VKM B-512) (bacteria)
Strain: ATCC 14581 / DSM 32 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / VKM B-512
Gene: cyp102A1, cyp102, BG04_163 / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase

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Non-polymers , 6 types, 657 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO2
#5: Chemical
ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO2
#6: Chemical
ChemComp-PHQ / benzyl chlorocarbonate / Benzyl chloroformate


Mass: 170.593 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H7ClO2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 52.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 75mM Tris-HCl (pH7.9), 0.1% (v/v) dimethyl sulfoxide, 0.1mM Benzyloxycarbonyl-L-prolyl-L-phenylalanine, 60mM 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: Nov 25, 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: 2.2→145.95 Å / Num. obs: 105865 / % possible obs: 97.1 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.366 / % possible all: 95.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DENZOdata collection
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACT3.22data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WSP

3wsp


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.78 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.253 5243 5 %RANDOM
Rwork0.221 ---
obs0.222 100612 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.02 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14620 0 304 637 15561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01915393
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214237
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.99220869
X-RAY DIFFRACTIONr_angle_other_deg0.9323.00233154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75151826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66824.839744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.012152723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7721580
X-RAY DIFFRACTIONr_chiral_restr0.0690.22213
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02117042
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023102
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 358 -
Rwork0.265 7167 -
obs--93.19 %

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