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- PDB-1smi: A single mutation of P450 BM3 induces the conformational rearrang... -

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Basic information

Entry
Database: PDB / ID: 1smi
TitleA single mutation of P450 BM3 induces the conformational rearrangement seen upon substrate-binding in wild-type enzyme
ComponentsBifunctional P-450:NADPH-P450 reductase
KeywordsOXIDOREDUCTASE / monooxygenase / fatty acid oxygenase / cytochrome P450 / substrate binding
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 / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9424
Polymers107,7092
Non-polymers1,2332
Water8,863492
1
A: Bifunctional P-450:NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4712
Polymers53,8541
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional P-450:NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4712
Polymers53,8541
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.206, 118.929, 146.338
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.47 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: PEG 2000, MME, 10mM Manganese sulphate, 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 1, 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→15 Å / Num. all: 68550 / Num. obs: 68550 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.051 / Net I/σ(I): 28.2
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2.41 / % possible all: 97.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.9999refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JPZ

1jpz


Resolution: 2→14.92 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.906 / SU B: 5.222 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.216 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28831 3440 5 %RANDOM
Rwork0.22376 ---
all0.22699 65010 --
obs0.22699 65010 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: 45.945 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→14.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7124 0 86 492 7702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0227387
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.98710021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9065888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3324.718354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.131151275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9631539
X-RAY DIFFRACTIONr_chiral_restr0.1140.21072
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025649
X-RAY DIFFRACTIONr_nbd_refined0.2390.23870
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2605
X-RAY DIFFRACTIONr_metal_ion_refined0.0130.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.218
X-RAY DIFFRACTIONr_mcbond_it1.1251.54621
X-RAY DIFFRACTIONr_mcangle_it1.68327177
X-RAY DIFFRACTIONr_scbond_it2.56833177
X-RAY DIFFRACTIONr_scangle_it3.7194.52841
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.329 274
Rwork0.273 4818

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