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- PDB-5zlh: Crystal structure of Mn-ProtoporphyrinIX-reconstituted P450BM3 -

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Basic information

Entry
Database: PDB / ID: 5zlh
TitleCrystal structure of Mn-ProtoporphyrinIX-reconstituted P450BM3
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 / 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
MANGANESE PROTOPORPHYRIN IX / Bifunctional cytochrome P450/NADPH--P450 reductase / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.4 Å
AuthorsOmura, K. / Aiba, Y. / Onoda, H. / Sugimoto, H. / Shoji, O. / Watanabe, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR15P3 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)17H03087 Japan
CitationJournal: Chem. Commun. (Camb.) / Year: 2018
Title: Reconstitution of full-length P450BM3 with an artificial metal complex by utilising the transpeptidase Sortase A.
Authors: Omura, K. / Aiba, Y. / Onoda, H. / Stanfield, J.K. / Ariyasu, S. / Sugimoto, H. / Shiro, Y. / Shoji, O. / Watanabe, Y.
History
DepositionMar 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Bifunctional cytochrome P450/NADPH--P450 reductase
D: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,1408
Polymers208,6784
Non-polymers2,4624
Water0
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7852
Polymers52,1691
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7852
Polymers52,1691
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7852
Polymers52,1691
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7852
Polymers52,1691
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.760, 155.320, 208.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 52169.461 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: BTA37_15100 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A1Q8UP87, UniProt: P14779*PLUS, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Chemical
ChemComp-MNH / MANGANESE PROTOPORPHYRIN IX


Mass: 615.580 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32MnN4O4

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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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M magnesium chloride, 12% PEG 3350, 0.1 M MES buffer (pH 6.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1.75 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.75 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 24522 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 47.99 Å2 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.053 / Rrim(I) all: 0.144 / Χ2: 0.885 / Net I/σ(I): 6 / Num. measured all: 180735
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
3.4-3.527.41.0824170.7380.4261.1620.991
3.52-3.667.40.76824150.830.3020.8260.963
3.66-3.837.40.53924100.9060.2110.5790.908
3.83-4.037.40.39724100.9170.1560.4271.144
4.03-4.287.40.23124570.9810.090.2480.766
4.28-4.617.40.14824250.9920.0580.1590.787
4.61-5.087.40.12324420.9920.0480.1320.773
5.08-5.817.40.12324610.9920.0480.1330.813
5.81-7.327.40.0924910.9960.0360.0970.837
7.32-507.10.04825940.9970.020.0520.878

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
RefinementResolution: 3.4→19.929 Å / SU ML: 0.65 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.36
RfactorNum. reflection% reflection
Rfree0.3462 1147 5.08 %
Rwork0.3103 --
obs0.3121 22572 95.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 164.1 Å2 / Biso mean: 42.8864 Å2 / Biso min: 1.84 Å2
Refinement stepCycle: final / Resolution: 3.4→19.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14550 0 172 0 14722
Biso mean--20.93 --
Num. residues----1804
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4001-3.5540.3761930.39151765185864
3.554-3.74020.49061490.42922744289398
3.7402-3.97280.4811590.39127442903100
3.9728-4.27670.36151510.335527962947100
4.2767-4.7020.31771480.290127972945100
4.702-5.37070.27371560.28528012957100
5.3707-6.72310.3441540.297828402994100
6.7231-19.9290.22311370.201329383075100

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