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- PDB-4kpb: Crystal structure of cytochrome P450 BM-3 R47E mutant -

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Basic information

Entry
Database: PDB / ID: 4kpb
TitleCrystal structure of cytochrome P450 BM-3 R47E mutant
ComponentsCytochrome P450 BM-3
KeywordsOXIDOREDUCTASE / heme-dependent stereospecific oxidation of substrates
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 / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSadre-Bazzaz, K. / Catalano, J. / McDermott, A.E. / Tong, L.
CitationJournal: Biochemistry / Year: 2013
Title: Structural Evidence: A Single Charged Residue Affects Substrate Binding in Cytochrome P450 BM-3.
Authors: Catalano, J. / Sadre-Bazzaz, K. / Amodeo, G.A. / Tong, L. / McDermott, A.
History
DepositionMay 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 BM-3
B: Cytochrome P450 BM-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,2094
Polymers112,9762
Non-polymers1,2332
Water13,908772
1
A: Cytochrome P450 BM-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1052
Polymers56,4881
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 BM-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1052
Polymers56,4881
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.963, 152.716, 62.003
Angle α, β, γ (deg.)90.00, 94.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 BM-3 / Bifunctional P-450/NADPH-P450 reductase / Cytochrome P450(BM-3) / Cytochrome P450 102


Mass: 56488.145 Da / Num. of mol.: 2 / Fragment: UNP residues 1-471 / Mutation: R47E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: cyp102A1, cyp102 / Production host: Escherichia coli (E. coli) / References: UniProt: P14779, unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 772 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 150 mM magnesium chloride, 100 mM MES, pH 6.0, 14% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2011 / Details: vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 63800 / Num. obs: 63450 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 17.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 6.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CBASSdata collection
COMOphasing
PHENIX(phenix.refine: 1.7_650)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.395 Å / SU ML: 0.3 / σ(F): 1.35 / Phase error: 22.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 3206 5.07 %RANDOM
Rwork0.1859 ---
obs0.1883 63247 99.46 %-
all-63800 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.114 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.8623 Å20 Å21.8843 Å2
2---1.8752 Å20 Å2
3---3.7376 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.395 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7118 0 86 772 7976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087393
X-RAY DIFFRACTIONf_angle_d1.15310019
X-RAY DIFFRACTIONf_dihedral_angle_d15.7672775
X-RAY DIFFRACTIONf_chiral_restr0.081072
X-RAY DIFFRACTIONf_plane_restr0.0041297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13130.30821290.21622591X-RAY DIFFRACTION99
2.1313-2.16460.26391500.21282644X-RAY DIFFRACTION100
2.1646-2.20010.27521170.19612602X-RAY DIFFRACTION100
2.2001-2.2380.26291350.19712619X-RAY DIFFRACTION100
2.238-2.27870.22861530.19052626X-RAY DIFFRACTION100
2.2787-2.32250.2451450.19132591X-RAY DIFFRACTION100
2.3225-2.36990.23151530.17942617X-RAY DIFFRACTION100
2.3699-2.42140.26411410.18662592X-RAY DIFFRACTION100
2.4214-2.47770.27551480.18542632X-RAY DIFFRACTION100
2.4777-2.53970.24761380.19882607X-RAY DIFFRACTION100
2.5397-2.60830.25471380.19332609X-RAY DIFFRACTION100
2.6083-2.6850.25391490.19242641X-RAY DIFFRACTION100
2.685-2.77160.24731390.19332608X-RAY DIFFRACTION100
2.7716-2.87060.25751390.19452594X-RAY DIFFRACTION100
2.8706-2.98540.23361270.19472651X-RAY DIFFRACTION100
2.9854-3.12110.22671360.18772646X-RAY DIFFRACTION100
3.1211-3.28550.23821320.19192626X-RAY DIFFRACTION100
3.2855-3.4910.21791470.18752604X-RAY DIFFRACTION100
3.491-3.76010.20191390.18682598X-RAY DIFFRACTION99
3.7601-4.13750.19061260.1652633X-RAY DIFFRACTION99
4.1375-4.73410.17561540.15362594X-RAY DIFFRACTION99
4.7341-5.95630.25591400.18212599X-RAY DIFFRACTION98
5.9563-29.39830.2571310.19922517X-RAY DIFFRACTION94

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