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- PDB-7yda: Crystal structure of the P450 BM3 heme domain mutant F87V/T268V/A... -

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Basic information

Entry
Database: PDB / ID: 7yda
TitleCrystal structure of the P450 BM3 heme domain mutant F87V/T268V/A184V in complex with N-imidazolyl-pentanoyl-L-phenylalanine 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 / 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
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: 1.557 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 4, 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)109,0068
Polymers107,0762
Non-polymers1,9306
Water19,1501063
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5034
Polymers53,5381
Non-polymers9653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-21 kcal/mol
Surface area19040 Å2
MethodPISA
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5034
Polymers53,5381
Non-polymers9653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-21 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.505, 147.013, 64.541
Angle α, β, γ (deg.)90.000, 99.960, 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: 53538.086 Da / Num. of mol.: 2 / Mutation: F87V,A184V,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
#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-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
#4: Chemical ChemComp-HOA / HYDROXYAMINE


Mass: 33.030 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H3NO / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1063 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
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 EIGER2 X 9M / Detector: PIXEL / Date: Nov 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.557→73.51 Å / Num. obs: 271644 / % possible obs: 96.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 20.81 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.039 / Rrim(I) all: 0.073 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.6 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.56-1.640.44977754213470.7940.2720.5262.595.8
4.92-73.510.0361712247110.9960.0220.04228.296

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FAG

1fag


Resolution: 1.557→39.434 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1983 3677 1.35 %
Rwork0.168 267967 -
obs0.1684 271644 89.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.67 Å2 / Biso mean: 27.1611 Å2 / Biso min: 9.36 Å2
Refinement stepCycle: final / Resolution: 1.557→39.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7322 0 234 1063 8619
Biso mean--18.51 38.83 -
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 (%)
1.557-1.57720.29151410.25571038889
1.5772-1.59880.23171400.24351029691
1.5988-1.62160.25931490.23411058691
1.6216-1.64580.24971450.23051042191
1.6458-1.67160.26971480.23071054491
1.6716-1.6990.24861390.21521048591
1.699-1.72830.20191420.20921048691
1.7283-1.75970.22941440.20661047691
1.7597-1.79350.26521440.21461035590
1.7935-1.83010.24711380.20181031190
1.8301-1.86990.21351370.19321013288
1.8699-1.91340.20171440.18141021789
1.9134-1.96130.2011440.17311046490
1.9613-2.01430.20211470.17041034290
2.0143-2.07360.18451450.16981029290
2.0736-2.14050.21551400.16441020088
2.1405-2.2170.191390.16131005188
2.217-2.30580.22631350.16241019988
2.3058-2.41070.21721360.1691010788
2.4107-2.53780.21881350.17221008388
2.5378-2.69670.21621350.17651014688
2.6967-2.90490.21461390.17661015388
2.9049-3.19710.2171360.16861020989
3.1971-3.65940.18511430.14871012788
3.6594-4.60940.14761450.13351039490
4.6094-39.40.15771470.15221050391
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)
11.4563-0.2560.86460.6522-0.27221.39220.0057-0.1103-0.08570.0680.0240.03370.0557-0.0678-0.03760.156-0.0130.01060.15970.00220.1406-1.9721-12.021624.8574
21.340.3917-0.55461.1647-0.30340.97210.0111-0.19530.21950.2049-0.02770.0333-0.1089-0.0003-0.00120.19790.01-0.02020.1475-0.04150.20310.512312.194118.5973
36.0561-0.29060.17740.34750.02180.3215-0.08550.05590.2838-0.01420.05170.1049-0.0643-0.07330.03830.2043-0.0054-0.01720.14510.01770.2004-6.64324.967111.5408
40.66510.2584-0.06870.8639-0.15260.61820.00660.0516-0.0319-0.03430.0072-0.06210.0260.0374-0.00880.13070.0128-0.00870.1404-0.0130.144310.4143-4.96739.8394
52.1969-0.1666-1.51910.73880.33113.41310.05250.19710.2335-0.02920.0369-0.0114-0.20170.0699-0.07780.2003-0.0089-0.01150.17180.04630.2301-14.6217-8.8232-26.4871
61.8385-0.88390.2761.2823-0.37280.36340.01660.0466-0.1510.02490.00260.02210.0446-0.0209-0.0290.1551-0.0163-0.00180.1335-0.02770.167-18.8643-32.4915-10.5336
71.15210.11490.07941.5917-1.29141.5694-0.06070.3992-0.2514-0.45380.005-0.03740.3329-0.01450.04930.3428-0.02970.04430.2822-0.11230.2861-22.7723-37.2803-25.3661
86.42730.3168-0.23410.22270.06120.3616-0.06760.0403-0.24890.02560.0350.08670.0656-0.06390.04830.2205-0.00310.02120.16640.00660.2022-24.642-31.2186-10.199
91.1705-0.4580.52041.0034-0.64291.0314-0.0068-0.00120.11290.0907-0.0072-0.0048-0.14410.03040.0350.1904-0.01650.00760.1608-0.02770.1675-9.3418-18.7617-7.0818
102.5835-1.34051.14412.3665-0.98092.85410.13430.1242-0.0695-0.23390.0036-0.00850.2282-0.0142-0.10860.1545-0.0295-0.00410.1664-0.02760.17670.4708-33.537-13.8824
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 108 )A3 - 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 456 )A283 - 456
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 72 )B3 - 72
6X-RAY DIFFRACTION6chain 'B' and (resid 73 through 158 )B73 - 158
7X-RAY DIFFRACTION7chain 'B' and (resid 159 through 226 )B159 - 226
8X-RAY DIFFRACTION8chain 'B' and (resid 227 through 282 )B227 - 282
9X-RAY DIFFRACTION9chain 'B' and (resid 283 through 424 )B283 - 424
10X-RAY DIFFRACTION10chain 'B' and (resid 425 through 456 )B425 - 456

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