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- PDB-4hgf: Crystal structure of P450 BM3 5F5K heme domain variant complexed ... -

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Basic information

Entry
Database: PDB / ID: 4hgf
TitleCrystal structure of P450 BM3 5F5K heme domain variant complexed with styrene
ComponentsBifunctional P-450/NADPH-P450 reductase
KeywordsOXIDOREDUCTASE / P450 BM3 / hemoprotein / styrene epoxidation / inverted enantioselectivity / Heme binding
Function / homology
Function and homology information


aromatase activity / 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 / 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 / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Cytochrome p450 / Cytochrome P450 / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. ...Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Cytochrome p450 / Cytochrome P450 / 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 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / 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 / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / ethenylbenzene / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsShehzad, A. / Panneerselvam, S. / Bocola, M. / Mueller-Dieckmann, J. / Wilmanns, M. / Schwaneberg, U.
Citation
Journal: Chem.Commun.(Camb.) / Year: 2013
Title: P450 BM3 crystal structures reveal the role of the charged surface residue Lys/Arg184 in inversion of enantioselective styrene epoxidation.
Authors: Shehzad, A. / Panneerselvam, S. / Linow, M. / Bocola, M. / Roccatano, D. / Mueller-Dieckmann, J. / Wilmanns, M. / Schwaneberg, U.
#1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2006
Title: A screening system for the directed evolution of epoxygenases: importance of position 184 in P450 BM3 for stereoselective styrene epoxidation.
Authors: Tee, K.L. / Schwaneberg, U.
History
DepositionOct 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Sep 20, 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 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_site / _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: Bifunctional P-450/NADPH-P450 reductase
B: Bifunctional P-450/NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7207
Polymers104,2432
Non-polymers1,4775
Water15,655869
1
A: Bifunctional P-450/NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8784
Polymers52,1211
Non-polymers7563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bifunctional P-450/NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8423
Polymers52,1211
Non-polymers7212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.138, 148.125, 64.066
Angle α, β, γ (deg.)90.00, 98.16, 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) / Cytochrome P450BM-3 / Cytochrome P450 102 / NADPH--cytochrome P450 reductase


Mass: 52121.441 Da / Num. of mol.: 2 / Fragment: Heme-binding domain / Mutation: F87A, A184K, T235A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: cyp102, cyp102A1 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SYN / ethenylbenzene / styrene


Mass: 104.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 869 / 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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 300 mM magnesium formate, 100 mM tris(hydroxymethyl)aminomethane (pH 8.5), 200 mM sodium malonate/110 mM potassium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 27, 2010 / Details: mirrors
RadiationMonochromator: Si 111 HORIZONTALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.7→19.51 Å / Num. all: 119333 / Num. obs: 117395 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 5 / Redundancy: 3.3 % / Biso Wilson estimate: 27.49 Å2 / Net I/σ(I): 10.99
Reflection shellResolution: 1.7→1.781 Å / Num. unique all: 15432 / % possible all: 99.2

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Processing

Software
NameVersionClassification
DNAdata collection
Auto-Rickshawphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J4S

2j4s


Resolution: 1.7→19.51 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22782 811 0.7 %RANDOM
Rwork0.18938 ---
obs0.18964 117395 98.31 %-
all-119333 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.141 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.04 Å2
2---0 Å20 Å2
3---0.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.103 Å0.101 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7117 0 103 869 8089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.027499
X-RAY DIFFRACTIONr_angle_refined_deg2.6671.98910176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9355913
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48324.86358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.858151370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4131539
X-RAY DIFFRACTIONr_chiral_restr0.1560.21087
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215709
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 67 -
Rwork0.35 8602 -
obs-8669 99.27 %

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