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- PDB-8qze: Heme-domain BM3 variant 21B3_F87V-A328F -

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Basic information

Entry
Database: PDB / ID: 8qze
TitleHeme-domain BM3 variant 21B3_F87V-A328F
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / CYP / cytochrome P450 / BM3 / CYP102A1 / BM3 T268E / CYP102 T268E
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 / 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 ...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 / 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
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsOpperman, D.J. / Ebrecht, A.C. / Aschenbrenner, J.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Science and Technology Funding CouncilST/R002754/1 United Kingdom
CitationJournal: Mol Catal / Year: 2024
Title: Revisiting strategies and their combinatorial effect for introducing peroxygenase activity in CYP102A1 (P450BM3)
Authors: Aschenbrenner, J.C. / Ebrecht, A.C. / Smit, M.S. / Opperman, D.J.
History
DepositionOct 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional cytochrome P450/NADPH--P450 reductase
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0137
Polymers106,5492
Non-polymers1,4635
Water4,864270
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0524
Polymers53,2751
Non-polymers7783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9603
Polymers53,2751
Non-polymers6862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.820, 127.200, 64.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Bifunctional cytochrome P450/NADPH--P450 reductase


Mass: 53274.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (bacteria) / Gene: cyp102A1 / Production host: Escherichia (bacteria) / References: UniProt: P14779
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M ammonium tartrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.87→137 Å / Num. obs: 164294 / % possible obs: 99.4 % / Redundancy: 8.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.089 / Net I/σ(I): 9.09
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.87-1.921.308121190.3941.5581
1.92-1.971118640.4631.21
1.97-2.030.714115720.6330.8461
2.03-2.090.624111720.680.7421
2.09-2.160.456108830.7880.5451
2.16-2.240.361105240.8760.4291
2.24-2.320.291101250.9010.3461
2.32-2.410.22297340.9390.2651
2.41-2.520.18393550.9630.2171
2.52-2.640.15189480.9740.1781
2.64-2.790.11985490.9820.1421
2.79-2.960.08980420.9910.1051
2.96-3.160.0775430.9930.0831
3.16-3.410.05770100.9940.0681
3.41-3.740.04964200.9960.0591
3.74-4.180.04457700.9960.0521
4.18-4.830.04251080.9960.051
4.83-5.910.04143560.9960.0491
5.91-8.360.03533460.9970.0421
8.36-1370.02918540.9980.0341

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XSCALEdata scaling
xia2data reduction
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→89.61 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.49 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20371 4364 5.1 %RANDOM
Rwork0.17042 ---
obs0.1722 81782 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.259 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å2-0 Å2
2---1.58 Å20 Å2
3---0.88 Å2
Refinement stepCycle: 1 / Resolution: 1.87→89.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7332 0 102 270 7704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127644
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167253
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.8710362
X-RAY DIFFRACTIONr_angle_other_deg0.5941.78916750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5335912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.502542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.177101361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.21108
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028925
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021731
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_it3.2133.83642
X-RAY DIFFRACTIONr_mcbond_other3.2123.83642
X-RAY DIFFRACTIONr_mcangle_it4.1266.8184553
X-RAY DIFFRACTIONr_mcangle_other4.1266.8194554
X-RAY DIFFRACTIONr_scbond_it4.4354.2384002
X-RAY DIFFRACTIONr_scbond_other4.4354.2384003
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6517.5625809
X-RAY DIFFRACTIONr_long_range_B_refined7.59737.188586
X-RAY DIFFRACTIONr_long_range_B_other7.59237.078555
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 302 -
Rwork0.312 5975 -
obs--99.95 %

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