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- PDB-1smj: Structure of the A264E mutant of cytochrome P450 BM3 complexed wi... -

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Basic information

Entry
Database: PDB / ID: 1smj
TitleStructure of the A264E mutant of cytochrome P450 BM3 complexed with palmitoleate
ComponentsBifunctional P-450:NADPH-P450 reductase
KeywordsOXIDOREDUCTASE / monooxygenase / fatty acid oxygenase / cytochrome P450 / substrate binding / palmitoleate
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 / 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 / PALMITOLEIC ACID / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsJoyce, M.G. / Girvan, H.M. / Munro, A.W. / Leys, D.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: A Single Mutation in Cytochrome P450 BM3 Induces the Conformational Rearrangement Seen upon Substrate Binding in the Wild-type Enzyme
Authors: Joyce, M.G. / Girvan, H.M. / Munro, A.W. / Leys, D.
History
DepositionMar 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
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.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional P-450:NADPH-P450 reductase
B: Bifunctional P-450:NADPH-P450 reductase
C: Bifunctional P-450:NADPH-P450 reductase
D: Bifunctional P-450:NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,90112
Polymers215,4174
Non-polymers3,4848
Water00
1
A: Bifunctional P-450:NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7253
Polymers53,8541
Non-polymers8712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional P-450:NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7253
Polymers53,8541
Non-polymers8712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bifunctional P-450:NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7253
Polymers53,8541
Non-polymers8712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bifunctional P-450:NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7253
Polymers53,8541
Non-polymers8712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.312, 166.886, 224.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: Protein
Bifunctional P-450:NADPH-P450 reductase / E.C.1.14.14.1 / Cytochrome P450(BM-3) / P450BM-3 [Includes: Cytochrome P450 102 / NADPH--cytochrome P450 reductase] ...Cytochrome P450(BM-3) / P450BM-3 [Includes: Cytochrome P450 102 / NADPH--cytochrome P450 reductase] / / cytochrome P-450:NADPH-P-450 reductase


Mass: 53854.328 Da / Num. of mol.: 4 / Fragment: cytochrome P450 102 / Mutation: A264E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P14779, unspecific monooxygenase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H30O2

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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: 2.41 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: PEG 2000, MME, 100mM magnesium acetate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 15, 2003
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→15 Å / Num. all: 53600 / Num. obs: 53600 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.069 / Net I/σ(I): 30.9
Reflection shellResolution: 2.7→2.82 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 3.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FAG

1fag


Resolution: 2.75→15 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.852 / SU B: 24.234 / SU ML: 0.478 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.521 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.33848 2645 5.1 %RANDOM
Rwork0.25319 ---
all0.25751 49263 --
obs0.25751 49263 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.694 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.75→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14669 0 244 0 14913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.02215281
X-RAY DIFFRACTIONr_angle_refined_deg2.9331.99220700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.89951815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.1224.879742
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.311152707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6921580
X-RAY DIFFRACTIONr_chiral_restr0.1760.22198
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211648
X-RAY DIFFRACTIONr_nbd_refined0.3260.28674
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2420.2748
X-RAY DIFFRACTIONr_metal_ion_refined0.2060.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3480.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.24
X-RAY DIFFRACTIONr_mcbond_it1.4171.59551
X-RAY DIFFRACTIONr_mcangle_it2.358214722
X-RAY DIFFRACTIONr_scbond_it3.74936753
X-RAY DIFFRACTIONr_scangle_it5.7194.55974
LS refinement shellResolution: 2.75→2.819 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.506 187
Rwork0.396 3321

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