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- PDB-7w97: Crystal Structure of the CYP102A1 (P450BM3) Heme Domain with N-He... -

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Basic information

Entry
Database: PDB / ID: 7w97
TitleCrystal Structure of the CYP102A1 (P450BM3) Heme Domain with N-Hexadecanoyl-L-Homoserine
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / CYTOCHROME P450
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 / 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
Chem-8PD / PROTOPORPHYRIN IX CONTAINING FE / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsKarasawa, M. / Stanfield, J.K. / Kasai, C. / Sugimoto, H. / Shoji, O.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP15H05806 Japan
Japan Society for the Promotion of Science (JSPS)JP19J23669 Japan
Japan Society for the Promotion of Science (JSPS)JP21H04704 Japan
Japan Science and TechnologyJPMJCR15P3 Japan
CitationJournal: To Be Published
Title: Crystal Structure of the CYP102A1 (P450BM3) Heme Domain with N-Hexadecanoyl-L-Homoserine
Authors: Karasawa, M. / Stanfield, J.K. / Kasai, C. / Sugimoto, H. / Shoji, O.
History
DepositionDec 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)106,7348
Polymers104,6012
Non-polymers2,1326
Water15,205844
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.677, 145.510, 62.934
Angle α, β, γ (deg.)90.000, 97.270, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 4 - 455 / Label seq-ID: 5 - 456

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Bifunctional cytochrome P450/NADPH--P450 reductase / Cytochrome P450(BM-3) / Cytochrome P450BM-3 / Fatty acid monooxygenase / Flavocytochrome P450 BM3


Mass: 52300.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (bacteria) / Gene: cyp102A1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-8PD / (2~{S})-2-(hexadecanoylamino)-4-oxidanyl-butanoic acid


Mass: 357.528 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H39NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 844 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 9%(w/v) PEG8000, 59 mM Magnesium Chloride, 74 mM Tris-HCl, 128 uM N-Hexadecanoyl-L-Homoserine, 1.3%(v/v) Methanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→48.5 Å / Num. obs: 204864 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.024 / Rrim(I) all: 0.065 / Net I/σ(I): 19.6 / Num. measured all: 1538527
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.4-1.427.41.22474475100740.5610.4831.3171.6100
7.67-48.57.50.0199677129210.0070.02172.899.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.557
Highest resolutionLowest resolution
Rotation45.54 Å1.75 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.7data scaling
MOLREPphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZO9

1zo9


Resolution: 1.4→45.59 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.012 / SU ML: 0.039 / SU R Cruickshank DPI: 0.0514 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1767 10139 5 %RANDOM
Rwork0.1579 ---
obs0.1589 194674 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.15 Å2 / Biso mean: 18.219 Å2 / Biso min: 9.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å2-0.39 Å2
2---0.04 Å2-0 Å2
3---0.69 Å2
Refinement stepCycle: final / Resolution: 1.4→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7294 0 234 844 8372
Biso mean--16.48 27.03 -
Num. residues----904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137779
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177229
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.70510564
X-RAY DIFFRACTIONr_angle_other_deg1.4871.62116727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3995.045927
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68723.462413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.506151355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.161540
X-RAY DIFFRACTIONr_chiral_restr0.0840.2950
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029534
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021690
Refine LS restraints NCS

Ens-ID: 1 / Number: 15526 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 775 -
Rwork0.264 14320 -
all-15095 -
obs--99.94 %

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