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- PDB-9l7v: Crystal structure of P450 BM3 F87A/V78G mutant complex with (-)-A... -

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Basic information

Entry
Database: PDB / ID: 9l7v
TitleCrystal structure of P450 BM3 F87A/V78G mutant complex with (-)-Ambroxide
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / cytochrome p450
Function / homology
Function and homology information


aromatase activity / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / unspecific monooxygenase / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme 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 / 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
Similarity search - Domain/homology
: / PROTOPORPHYRIN IX CONTAINING FE / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsDong, S. / Feng, Y.G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071266 China
National Natural Science Foundation of China (NSFC)32171203 China
CitationJournal: To Be Published
Title: Crystal structure of P450 BM3 F87A/V78G mutant complex with (-)-Ambroxide
Authors: Dong, S. / Feng, Y.G.
History
DepositionDec 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 7, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)106,0716
Polymers104,3652
Non-polymers1,7064
Water11,422634
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0353
Polymers52,1821
Non-polymers8532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-22 kcal/mol
Surface area19290 Å2
MethodPISA
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0353
Polymers52,1821
Non-polymers8532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-22 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.650, 148.300, 64.670
Angle α, β, γ (deg.)90.00, 100.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 52182.484 Da / Num. of mol.: 2 / Mutation: V79S,F88A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: F2Q7T0, 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1EI5 / (3~{a}~{R},5~{a}~{S},9~{a}~{S},9~{b}~{R})-3~{a},6,6,9~{a}-tetramethyl-2,4,5,5~{a},7,8,9,9~{b}-octahydro-1~{H}-benzo[e][1]benzofuran / (-)-ambroxide


Mass: 236.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H28O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH7.5, and 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.02→74.15 Å / Num. obs: 68943 / % possible obs: 97.2 % / Redundancy: 3 % / CC1/2: 0.98 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.123 / Rrim(I) all: 0.22 / Χ2: 0.94 / Net I/σ(I): 5.8 / Num. measured all: 205806
Reflection shellResolution: 2.02→2.07 Å / % possible obs: 95.9 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.672 / Num. measured all: 11657 / Num. unique obs: 5012 / CC1/2: 0.366 / Rpim(I) all: 0.537 / Rrim(I) all: 0.865 / Χ2: 0.71 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→28.22 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2697 3355 4.88 %
Rwork0.2308 --
obs0.2327 68719 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→28.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7179 0 120 634 7933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027483
X-RAY DIFFRACTIONf_angle_d0.56110173
X-RAY DIFFRACTIONf_dihedral_angle_d7.4361008
X-RAY DIFFRACTIONf_chiral_restr0.0381090
X-RAY DIFFRACTIONf_plane_restr0.0041322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.050.39591350.34182674X-RAY DIFFRACTION96
2.05-2.080.39911370.35052646X-RAY DIFFRACTION95
2.08-2.110.35391430.3282643X-RAY DIFFRACTION95
2.11-2.150.35281320.30922710X-RAY DIFFRACTION95
2.15-2.180.39271480.3072674X-RAY DIFFRACTION95
2.18-2.220.34321360.31012682X-RAY DIFFRACTION96
2.22-2.270.38561410.35042649X-RAY DIFFRACTION94
2.27-2.310.32781390.29672774X-RAY DIFFRACTION98
2.31-2.360.31521210.27892735X-RAY DIFFRACTION97
2.36-2.420.30851450.25722782X-RAY DIFFRACTION99
2.42-2.480.30031470.25422788X-RAY DIFFRACTION99
2.48-2.540.32451220.24752776X-RAY DIFFRACTION99
2.54-2.620.29351330.23972803X-RAY DIFFRACTION99
2.62-2.70.31420.23682784X-RAY DIFFRACTION98
2.7-2.80.26511490.23542778X-RAY DIFFRACTION99
2.8-2.910.26581630.22462736X-RAY DIFFRACTION99
2.91-3.050.23831430.21962792X-RAY DIFFRACTION99
3.05-3.210.26731490.21372784X-RAY DIFFRACTION99
3.21-3.410.23561410.21442789X-RAY DIFFRACTION99
3.41-3.670.24111570.19892687X-RAY DIFFRACTION96
3.67-4.040.23061310.19072701X-RAY DIFFRACTION96
4.04-4.620.19921220.16862778X-RAY DIFFRACTION97
4.62-5.810.23931390.19382639X-RAY DIFFRACTION94
5.81-28.220.19541400.18432560X-RAY DIFFRACTION90
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6910.40460.21961.44570.73630.62640.0176-0.25620.04290.0165-0.012-0.0105-0.01790.03-0.00410.15590.02250.0120.15960.03280.161340.59576.036948.8714
24.64131.1681.11165.02532.45054.75620.0788-0.8056-0.31840.6253-0.25960.00950.1213-0.06640.13630.2217-0.031-0.01910.18130.05240.251841.1444-12.066951.9816
32.7528-0.13290.67121.14770.01110.28910.0576-0.4489-0.21540.14140.0298-0.33070.1159-0.0159-0.0630.24870.00020.00110.22680.00870.227849.258-4.844649.0481
42.20830.48640.57031.07630.37680.957-0.1260.0720.1632-0.11740.0470.1082-0.1381-0.00010.06960.16640.03370.030.10960.05740.161331.20976.749839.6428
52.027-0.11371.20980.91730.71122.36110.06050.2832-0.3143-0.012-0.0028-0.0601-0.03970.0536-0.07090.16090.0236-0.00440.1858-0.04040.191420.138512.45172.6471
62.8821-0.98530.04491.12360.39820.6045-0.01590.20860.1342-0.06350.03170.0318-0.07070.082-0.00830.1621-0.0425-0.04470.11450.02080.143524.28335.017819.9343
74.00410.229-0.58655.2459-0.35623.57430.13461.37250.3397-1.2479-0.04580.29420.3279-0.30050.06360.3290.0584-0.09910.51730.14650.427223.401140.24676.7272
81.8512-0.00110.15771.0796-0.13470.4565-0.03550.34440.7842-0.1235-0.0579-0.34-0.16230.18860.18420.2596-0.01210.04030.24540.0510.340631.543636.856615.4653
91.6651-0.60880.08491.44840.46641.10810.0126-0.0515-0.07770.1596-0.03980.09390.1223-0.03420.03720.1092-0.04080.01240.08850.0030.123213.072123.3921.2976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 158 )
2X-RAY DIFFRACTION2chain 'A' and (resid 159 through 186 )
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 282 )
4X-RAY DIFFRACTION4chain 'A' and (resid 283 through 455 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 72 )
6X-RAY DIFFRACTION6chain 'B' and (resid 73 through 158 )
7X-RAY DIFFRACTION7chain 'B' and (resid 159 through 195 )
8X-RAY DIFFRACTION8chain 'B' and (resid 196 through 282 )
9X-RAY DIFFRACTION9chain 'B' and (resid 283 through 455 )

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