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- PDB-7yft: Crystal structure of the P450 BM3 heme domain mutant F87A/T268V/A... -

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Basic information

Entry
Database: PDB / ID: 7yft
TitleCrystal structure of the P450 BM3 heme domain mutant F87A/T268V/A82C/L181M in complex with N-imidazolyl-pentanoyl-L-phenylalanine, indane and hydroxylamine
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / P450 BM3 heme domain
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
2,3-dihydro-1H-indene / PROTOPORPHYRIN IX CONTAINING FE / HYDROXYAMINE / Chem-IRV / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDong, S. / Chen, J. / Jiang, Y. / Cong, Z. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171203 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Regiodivergent and Enantioselective Hydroxylation of C-H bonds by Synergistic Use of Protein Engineering and Exogenous Dual-Functional Small Molecules.
Authors: Chen, J. / Dong, S. / Fang, W. / Jiang, Y. / Chen, Z. / Qin, X. / Wang, C. / Zhou, H. / Jin, L. / Feng, Y. / Wang, B. / Cong, Z.
History
DepositionJul 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)109,23010
Polymers107,0642
Non-polymers2,1668
Water12,016667
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A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6155
Polymers53,5321
Non-polymers1,0834
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-21 kcal/mol
Surface area18120 Å2
MethodPISA
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6155
Polymers53,5321
Non-polymers1,0834
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-20 kcal/mol
Surface area18010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.930, 143.730, 62.440
Angle α, β, γ (deg.)90.000, 100.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 53532.082 Da / Num. of mol.: 2 / Mutation: A82C,F87A,L181M,T268V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
Strain: ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19
Gene: cyp102A1, cyp102, BG04_163 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase

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Non-polymers , 5 types, 675 molecules

#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-HOA / HYDROXYAMINE / Hydroxylamine


Mass: 33.030 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H3NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-16N / 2,3-dihydro-1H-indene / indan / Vinzons


Mass: 118.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-IRV / (2~{S})-2-(5-imidazol-1-ylpentanoylamino)-3-phenyl-propanoic acid


Mass: 315.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 667 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.35 Å3/Da / Density % sol: 47.65 %
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, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→38.477 Å / Num. obs: 114919 / % possible obs: 87.2 % / Redundancy: 1.604 % / Biso Wilson estimate: 20.62 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.067 / Χ2: 1.427 / Net I/σ(I): 10.95 / Num. measured all: 184326
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
2-2.051.6520.1215.6214464975887550.9540.16789.7
2.05-2.111.6410.1056.4514112957085990.9660.14589.9
2.11-2.171.6330.0967.2113427917982230.9710.13389.6
2.17-2.241.620.0857.8312898901279610.9770.11888.3
2.24-2.311.60.088.5312283869976750.9790.11188.2
2.31-2.391.5780.0739.1111709838674200.9830.10288.5
2.39-2.481.590.0659.8911239821670700.9840.0986.1
2.48-2.581.6190.06110.5510962771467710.9850.08587.8
2.58-2.71.6030.05711.4210349754564560.9870.07985.6
2.7-2.831.5910.05112.329640713960590.9880.07184.9
2.83-2.981.5980.04813.139108681756990.9880.06883.6
2.98-3.161.5880.04714.118549645153840.9880.06683.5
3.16-3.381.5820.04214.988008599550610.9890.05984.4
3.38-3.651.5770.04215.697435567147160.9890.05983.2
3.65-41.5770.03916.036998516744380.9910.05585.9
4-4.471.5770.03616.346542470941490.9920.05188.1
4.47-5.161.5970.03816.385868413236740.990.05388.9
5.16-6.321.5820.03615.814957349231340.9920.0589.7
6.32-8.941.6030.03616.453866266824110.9930.05190.4
8.94-38.4771.5130.0316.451912147512640.9960.04385.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1fag

1fag


Resolution: 2→38.477 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 27.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 3625 3.15 %
Rwork0.2411 111272 -
obs0.2419 114897 87.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.44 Å2 / Biso mean: 29.7168 Å2 / Biso min: 7.2 Å2
Refinement stepCycle: final / Resolution: 2→38.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7253 0 306 667 8226
Biso mean--56.72 27.5 -
Num. residues----903
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02640.33331390.2826445989
2.0264-2.05410.3391390.2782433391
2.0541-2.08350.32981480.279454791
2.0835-2.11460.27421420.2695434289
2.1146-2.14760.31221420.271439890
2.1476-2.18280.3381440.2653432989
2.1828-2.22040.27021410.2583429788
2.2204-2.26080.26391390.2545438489
2.2608-2.30430.24891410.2539432888
2.3043-2.35130.31111420.2587432488
2.3513-2.40240.29851420.2654440789
2.4024-2.45830.31771450.2653417786
2.4583-2.51980.29691370.2611424087
2.5198-2.58790.27481460.2706431987
2.5879-2.6640.35191410.2646420686
2.664-2.750.29071320.242413385
2.75-2.84820.23831380.2585422184
2.8482-2.96220.27051320.2416406084
2.9622-3.0970.29221240.2453407983
3.097-3.26020.24351350.2355412585
3.2602-3.46430.21951340.2303413984
3.4643-3.73160.24511360.2173405883
3.7316-4.10680.24041390.21425887
4.1068-4.70010.22561360.1995434588
4.7001-5.91820.24021490.2265437089
5.9182-38.40.22461420.2311439489
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)
12.38180.7878-1.37770.5855-0.42561.5686-0.03720.34330.2545-0.03180.06330.0336-0.1286-0.0913-0.03130.15870.0186-0.02980.18150.04760.1913-19.7732-13.9564-21.8158
21.8782-0.62120.80141.46930.16161.64450.10610.265-0.2835-0.375-0.07770.1378-0.073-0.1114-0.05920.3040.0028-0.01470.1726-0.02190.3236-17.3718-37.7455-17.0855
34.98670.55320.03710.22870.2095-0.1921-0.0027-0.1697-0.47650.0457-0.03710.08750.05810.00950.02390.245-0.01110.05830.16660.04110.1942-24.0188-30.6375-9.6921
41.8726-0.33970.31591.2818-0.28521.002-0.0393-0.04520.23130.0820.0281-0.0947-0.10930.03530.00340.1458-0.0451-0.00720.10840.00180.1699-7.253-21.0324-8.0878
52.17760.38812.42150.57381.61395.5216-0.006-0.093-0.10620.0430.08480.15680.1683-0.053-0.08150.17250.0004-0.01540.12920.04420.21833.3383-16.23227.8736
62.51011.5311-0.3951.6066-0.54560.576-0.0572-0.02150.1802-0.00870.0836-0.0342-0.0909-0.0586-0.01030.15980.0493-0.03310.10350.00890.2369-0.73926.212811.2749
71.73761.4642-1.41471.5826-1.89711.92610.1835-0.5940.23280.6488-0.15630.0326-0.35430.12910.01120.4266-0.0055-0.02430.396-0.05240.3534-0.640810.22725.2782
81.35380.475-0.20741.1091-0.19280.7513-0.0037-0.04920.09810.09160.02830.0667-0.0973-0.05410.00320.16590.0133-0.04570.12950.00730.1954.0877-0.811411.9627
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 108 )A5 - 108
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 226 )A109 - 226
3X-RAY DIFFRACTION3chain 'A' and (resid 227 through 282 )A227 - 282
4X-RAY DIFFRACTION4chain 'A' and (resid 283 through 455 )A283 - 455
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 72 )B4 - 72
6X-RAY DIFFRACTION6chain 'B' and (resid 73 through 158 )B73 - 158
7X-RAY DIFFRACTION7chain 'B' and (resid 159 through 195 )B159 - 195
8X-RAY DIFFRACTION8chain 'B' and (resid 196 through 455 )B196 - 455

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