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- PDB-7w9j: Crystal Structure of the Oxomolybdenum Mesoporphyrin IX-Reconstit... -

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Basic information

Entry
Database: PDB / ID: 7w9j
TitleCrystal Structure of the Oxomolybdenum Mesoporphyrin IX-Reconstituted CYP102A1 (P450BM3) Heme Domain with N-Dodecanoyl-L-Homoserine Lactone
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 / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding ...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 / response to hormone / 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
N-[(3S)-2-oxooxolan-3-yl]dodecanamide / Oxomolybdenum Mesoporphyrin IX / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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 Oxomolybdenum Mesoporphyrin IX-Reconstituted CYP102A1 (P450BM3) Heme Domain with N-Dodecanoyl-L-Homoserine Lactone
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)106,7989
Polymers104,6012
Non-polymers2,1967
Water7,710428
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)58.295, 121.827, 148.689
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 2 - 454 / Label seq-ID: 3 - 455

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-MI9 / Oxomolybdenum Mesoporphyrin IX


Mass: 676.613 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H36MoN4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EWM / N-[(3S)-2-oxooxolan-3-yl]dodecanamide


Mass: 283.406 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H29NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 277 K / Method: batch mode
Details: 8.5%(w/v)PEG8000, 60 mM Magnesium Chloride, 75 mM Tris-HCl, 250 uM N-Dodecanoyl-L-Homoserine Lactone, 1%(v/v) Methanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→49.63 Å / Num. obs: 107242 / % possible obs: 99.1 % / Redundancy: 7.109 % / Biso Wilson estimate: 30.641 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.143 / Rrim(I) all: 0.154 / Χ2: 0.778 / Net I/σ(I): 9.29 / Num. measured all: 762372
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.856.7271.411.4711284717292167740.5811.52797
1.85-1.986.9790.872.5311231316256160920.810.93999
1.98-2.147.3110.524.2711028815194150850.920.55999.3
2.14-2.347.1380.3296.449955314038139460.9630.35499.3
2.34-2.626.8520.2298.588659312673126370.9790.24799.7
2.62-3.027.1610.15412.528055211279112480.9920.16699.7
3.02-3.77.490.09120.271809960195870.9970.09799.9
3.7-5.217.1430.06427.4553675753375140.9980.06999.7
5.21-49.637.970.05629.2134742437643590.9980.0699.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.555
Highest resolutionLowest resolution
Rotation49.58 Å1.99 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K58

6k58


Resolution: 1.75→49.63 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.885 / SU ML: 0.086 / SU R Cruickshank DPI: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2099 5329 5 %RANDOM
Rwork0.1781 ---
obs0.1797 101500 99.36 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.06 Å2 / Biso mean: 27.511 Å2 / Biso min: 10.77 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å2-0 Å20 Å2
2--2.13 Å2-0 Å2
3----0.98 Å2
Refinement stepCycle: final / Resolution: 1.75→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7335 0 146 428 7909
Biso mean--27.62 32.16 -
Num. residues----909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137671
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167240
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.67610394
X-RAY DIFFRACTIONr_angle_other_deg1.3361.59616747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4825909
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.10823.35412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.704151360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7141541
X-RAY DIFFRACTIONr_chiral_restr0.0760.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028561
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021685
Refine LS restraints NCS

Ens-ID: 1 / Number: 14922 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 396 -
Rwork0.347 7369 -
all-7765 -
obs--98.73 %

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