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- PDB-3hf2: Crystal structure of the I401P mutant of cytochrome P450 BM3 -

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Basic information

Entry
Database: PDB / ID: 3hf2
TitleCrystal structure of the I401P mutant of cytochrome P450 BM3
ComponentsBifunctional P-450/NADPH-P450 reductase
KeywordsOXIDOREDUCTASE / P450 FAMILY PROTEIN FOLD / Electron transport / FAD / Flavoprotein / FMN / Heme / Iron / Metal-binding / Monooxygenase / Multifunctional enzyme / NADP / Transport
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 / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYang, W. / Whitehouse, C.J.C. / Bell, S.G. / Bartlam, M. / Wong, L.L. / Rao, Z.
CitationJournal: Chembiochem / Year: 2009
Title: A Highly Active Single-Mutation Variant of P450(BM3) (CYP102A1)
Authors: Whitehouse, C.J.C. / Bell, S.G. / Yang, W. / Yorke, J.A. / Blanford, C.F. / Strong, A.J.F. / Morse, E.J. / Bartlam, M. / Rao, Z. / Wong, L.-L.
History
DepositionMay 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 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 1.3Nov 1, 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

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)111,2444
Polymers110,0112
Non-polymers1,2332
Water9,116506
1
A: Bifunctional P-450/NADPH-P450 reductase
B: Bifunctional P-450/NADPH-P450 reductase
hetero molecules

A: Bifunctional P-450/NADPH-P450 reductase
B: Bifunctional P-450/NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,4898
Polymers220,0234
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Unit cell
Length a, b, c (Å)58.670, 145.843, 63.229
Angle α, β, γ (deg.)90.00, 97.33, 90.00
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) / P450BM-3 / Cytochrome P450 102 /


Mass: 55005.641 Da / Num. of mol.: 2 / Fragment: heme domain, UNP residues 1-482 / Mutation: I401P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: P450BM-3 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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.: 506 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% PEG 3350, 0.2M magnesium chloride, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 53030 / Num. obs: 52999 / % possible obs: 99.15 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 2.7 / Num. unique all: 5029 / % possible all: 94.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0044refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1bu7

1bu7


Resolution: 2.2→45.48 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.917 / SU B: 12.654 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24472 2694 5.1 %RANDOM
Rwork0.18556 ---
obs0.18858 50305 99.15 %-
all-53030 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.943 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å2-0.29 Å2
2---0.77 Å20 Å2
3---2.21 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6872 0 86 506 7464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227126
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5862.0069653
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.315843
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61124.769346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25151271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3961538
X-RAY DIFFRACTIONr_chiral_restr0.1060.21031
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215412
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7631.54250
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42226859
X-RAY DIFFRACTIONr_scbond_it2.41632876
X-RAY DIFFRACTIONr_scangle_it3.8114.52794
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 182 -
Rwork0.226 3502 -
obs--92.61 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.52440.10480.04490.18080.07580.0730.0173-0.0375-0.0279-0.0127-0.0029-0.0022-0.00070.0005-0.01440.0178-0.00270.0050.00420.00620.033216.28920.088612.8377
20.3772-0.12120.0310.20920.10540.1162-0.00980.05160.05870.00590.0023-0.01010.00420.00510.00750.0147-0.0003-0.01440.01320.01020.0419-4.849123.337-14.2987
35.30433.09511.14511.80620.66710.2526-0.07430.1384-0.0596-0.03680.0765-0.0386-0.03720.0285-0.00220.0910.0022-0.06030.01640.00890.067422.06981.709411.3862
43.53812.27380.39181.6477-0.13290.8377-0.10910.2344-0.057-0.06470.1631-0.03390.0334-0.0798-0.0540.0281-0.0053-0.02660.0307-0.00510.07710.864421.8268-13.3362
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 455
2X-RAY DIFFRACTION2B5 - 455
3X-RAY DIFFRACTION3A482
4X-RAY DIFFRACTION4B482

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