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- PDB-7yje: Crystal structure of the P450 BM3 heme domain mutant F87G/T268V/A... -

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Basic information

Entry
Database: PDB / ID: 7yje
TitleCrystal structure of the P450 BM3 heme domain mutant F87G/T268V/A184V/A328V in complex with N-imidazolyl-hexanoyl-L-phenylalanine and acetate ion
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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Chem-IC6 / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 20, 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)109,0588
Polymers107,0482
Non-polymers2,0106
Water18,0511002
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A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5294
Polymers53,5241
Non-polymers1,0053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-21 kcal/mol
Surface area18940 Å2
MethodPISA
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5294
Polymers53,5241
Non-polymers1,0053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-21 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.699, 148.510, 64.097
Angle α, β, γ (deg.)90.000, 99.730, 90.000
Int Tables number4
Space group name H-MP1211

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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: 53524.055 Da / Num. of mol.: 2
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
#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-IC6 / (2S)-2-(6-imidazol-1-ylhexanoylamino)-3-phenyl-propanoic acid


Mass: 329.394 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H23N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1002 / 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: 2.57 Å3/Da / Density % sol: 52.18 %
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: BL17B1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 128081 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.045 / Rrim(I) all: 0.084 / Χ2: 0.917 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.883.40.5845360.70.3670.6880.86198.8
1.88-1.923.40.51744750.7440.3290.6150.87298.8
1.92-1.953.20.40845610.80.2660.4890.89298.6
1.95-1.9930.32644930.8450.2250.3980.88398.4
1.99-2.043.20.30545270.870.2020.3670.90899
2.04-2.083.60.26745690.9110.1650.3140.90599.8
2.08-2.143.60.22645890.940.1390.2660.89599.9
2.14-2.193.60.18945500.9570.1160.2220.90399.8
2.19-2.263.60.16346080.9650.1010.1920.94899.7
2.26-2.333.50.14445520.9710.0890.1690.92699.8
2.33-2.413.50.12645530.9770.0780.1490.93699.6
2.41-2.513.50.10645400.9820.0660.1250.92199
2.51-2.633.40.09245550.9840.0570.1090.93999
2.63-2.763.20.07645360.9880.0490.0910.89198.7
2.76-2.9430.06245570.990.0410.0750.91598.6
2.94-3.163.60.05945480.9930.0350.0681.00499.8
3.16-3.483.60.05146060.9940.0310.061.06599.9
3.48-3.993.60.04446170.9950.0270.0511.06699.8
3.99-5.023.40.03845780.9960.0230.0440.92499.5
5.02-503.50.03246290.9980.020.0380.64598.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1fag

1fag


Resolution: 1.85→46.786 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1858 2905 2.27 %
Rwork0.1463 125176 -
obs0.1472 128081 70.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.61 Å2 / Biso mean: 24.5665 Å2 / Biso min: 1.53 Å2
Refinement stepCycle: final / Resolution: 1.85→46.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7320 0 344 1002 8666
Biso mean--16.97 34.81 -
Num. residues----908
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8504-1.88080.3113700.2443300035
1.8808-1.91320.3009770.223329539
1.9132-1.9480.2194840.2072360842
1.948-1.98550.2203870.2022374244
1.9855-2.0260.2289940.1962409848
2.026-2.07010.20861000.1809432351
2.0701-2.11820.23411020.1771444153
2.1182-2.17120.19161120.1628474255
2.1712-2.22990.21991150.1503498059
2.2299-2.29550.17171220.1507544564
2.2955-2.36960.19311430.1489595970
2.3696-2.45430.18081450.1453653877
2.4543-2.55250.2061660.1424714184
2.5525-2.66870.2171730.1504737787
2.6687-2.80940.17541720.1515747488
2.8094-2.98540.20161770.1487781093
2.9854-3.21580.20411910.1413829698
3.2158-3.53930.15681910.1281826698
3.5393-4.05120.15861990.1206828898
4.0512-5.10310.14291900.1252812496
5.1031-460.2061950.1659822997
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)
10.9132-0.04530.44060.5699-0.18360.78590.0326-0.0904-0.07170.06270.02020.08390.0434-0.126-0.02980.1515-0.00380.01670.1713-0.01150.1223-1.5739-12.403524.6554
21.27620.3428-0.33031.5367-0.23350.93360.0055-0.19720.22960.2039-0.01440.0859-0.1169-0.0170.00710.15220.0021-0.0150.1211-0.03450.17380.806312.226418.509
31.9859-0.0345-0.01540.62590.12030.4175-0.1017-0.00760.2002-0.03230.07240.143-0.0672-0.12750.04510.19660.00990.00120.14660.01480.1736-6.31175.016411.4651
40.73750.2686-0.03761.5602-0.23830.6659-0.00910.0894-0.0385-0.18710.0371-0.0430.06970.0048-0.02720.12190.02190.00220.1298-0.02860.095810.7213-5.06589.8303
51.2651-0.1872-0.11061.2128-0.2930.7427-0.05330.23360.3328-0.0219-0.0011-0.0443-0.1637-0.04590.06680.1469-0.0036-0.02780.17990.02440.1886-14.6971-8.9339-26.3066
61.0544-0.54440.31931.0222-0.22140.4095-0.0602-0.044-0.02630.08820.05890.0642-0.0361-0.17190.01010.13150.02650.02590.1545-0.02770.1413-23.9065-29.4968-9.9233
70.8147-0.09960.54681.1403-0.67340.66580.02680.2321-0.1017-0.2071-0.0099-0.03090.09830.06980.01970.15960.0330.02160.1524-0.05480.1727-14.0912-38.5048-19.5176
81.54480.4206-0.9211.7461-1.75853.6758-0.10290.3805-0.2509-0.46870.19210.14510.545-0.09010.03460.2932-0.06010.01840.2948-0.14340.331-28.6417-38.8068-26.3071
92.3608-0.4993-0.37782.36420.79871.0605-0.1638-0.0055-0.29120.20460.05040.10740.2451-0.0842-0.04670.21040.03570.08850.2550.01010.2185-36.5248-33.2676-5.1418
100.9913-0.04150.21970.3451-0.28780.234-0.0668-0.07550.00080.10480.0486-0.0021-0.0591-0.05930.01850.15770.0368-0.00450.1221-0.04470.1039-10.2704-27.3363-6.6604
111.8587-0.30660.97861.6607-0.43471.2921-0.2829-0.02390.47260.42870.098-0.0536-0.3937-0.03790.13420.25950.0265-0.0610.1268-0.0470.2289-11.3306-8.149-13.6695
121.1002-0.11530.52210.9739-0.35581.0418-0.0690.01460.03860.07290.0508-0.023-0.111-0.03520.010.11290.0109-0.0030.1152-0.0440.0936-6.2538-29.0138-9.2451
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 108 )A2 - 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 2 through 72 )B2 - 72
6X-RAY DIFFRACTION6chain 'B' and (resid 73 through 131 )B73 - 131
7X-RAY DIFFRACTION7chain 'B' and (resid 132 through 195 )B132 - 195
8X-RAY DIFFRACTION8chain 'B' and (resid 196 through 226 )B196 - 226
9X-RAY DIFFRACTION9chain 'B' and (resid 227 through 250 )B227 - 250
10X-RAY DIFFRACTION10chain 'B' and (resid 251 through 335 )B251 - 335
11X-RAY DIFFRACTION11chain 'B' and (resid 336 through 384 )B336 - 384
12X-RAY DIFFRACTION12chain 'B' and (resid 385 through 455 )B385 - 455

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