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- PDB-7ydb: Crystal structure of the P450 BM3 heme domain mutant F87V/T268I i... -

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Basic information

Entry
Database: PDB / ID: 7ydb
TitleCrystal structure of the P450 BM3 heme domain mutant F87V/T268I in complex with N-imidazolyl-pentanoyl-L-phenylalanine,ethylbenzene and hydroxylamine
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / P450 BM3 heme domain
Function / homology
Function and homology information


aromatase activity / 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 / 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 / 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 / HYDROXYAMINE / Chem-IRV / PHENYLETHANE / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.472 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

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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)109,19010
Polymers107,0482
Non-polymers2,1428
Water23,4561302
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5955
Polymers53,5241
Non-polymers1,0714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-20 kcal/mol
Surface area18120 Å2
MethodPISA
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5955
Polymers53,5241
Non-polymers1,0714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-20 kcal/mol
Surface area17850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.053, 144.347, 62.741
Angle α, β, γ (deg.)90.000, 100.060, 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: 53524.059 Da / Num. of mol.: 2 / Mutation: F87V,T268I
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, 1310 molecules

#2: Chemical ChemComp-HOA / HYDROXYAMINE


Mass: 33.030 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H3NO / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-PYJ / PHENYLETHANE


Mass: 106.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10 / 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


Mass: 18.015 Da / Num. of mol.: 1302 / 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: 2.38 Å3/Da / Density % sol: 48.24 %
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: 1.47→72.17 Å / Num. obs: 290176 / % possible obs: 97.6 % / Redundancy: 2.7 % / Biso Wilson estimate: 17.21 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.032 / Rrim(I) all: 0.055 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.47-1.552.30.32154255235680.8410.2520.4112.596.1
4.66-72.172.60.0381324251100.9790.0290.04816.394.3

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Processing

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

1fag


Resolution: 1.472→45.725 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.192 3169 1.22 %
Rwork0.1653 286642 -
obs0.1656 290176 86.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.95 Å2 / Biso mean: 25.9797 Å2 / Biso min: 11.04 Å2
Refinement stepCycle: final / Resolution: 1.472→45.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7275 0 198 1302 8775
Biso mean--25.17 37.7 -
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 (%)
1.4721-1.49230.29731180.2716948672
1.4923-1.51360.28541240.2568974974
1.5136-1.53620.25471150.2489999675
1.5362-1.56020.25291210.23321039979
1.5602-1.58580.23461320.21991076781
1.5858-1.61310.25571410.22021133886
1.6131-1.64240.21951550.2111192890
1.6424-1.6740.22841480.19971195590
1.674-1.70820.21241540.19811191991
1.7082-1.74540.2071520.19851203890
1.7454-1.7860.2121460.19021193490
1.786-1.83060.24571480.18921193491
1.8306-1.88010.19861450.18431205091
1.8801-1.93540.16351490.17851196891
1.9354-1.99790.18511490.17271200491
1.9979-2.06930.20461470.16691193190
2.0693-2.15220.19111470.16551179889
2.1522-2.25010.20361470.16451172389
2.2501-2.36870.18711380.16181170989
2.3687-2.51710.22711390.16111168988
2.5171-2.71150.21671410.16421160288
2.7115-2.98430.16911520.1581180789
2.9843-3.4160.18491470.14111164389
3.416-4.30330.14071440.12741194790
4.3033-45.70.18291350.15841132886
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)
12.3106-0.2143-1.42870.93160.2683.33760.00980.29030.2615-0.0311-0.01320.0029-0.1542-0.0103-0.00620.14330.0029-0.00270.14840.06180.1814-14.3684-9.054-25.525
21.8262-0.9538-0.14541.61060.05240.34830.12850.2885-0.1895-0.2456-0.12420.05180.0582-0.07390.00320.158-0.00670.00150.1545-0.03680.1243-20.318-34.2183-16.6699
36.11370.0969-0.7290.34850.0530.4065-0.0107-0.0185-0.30980.0257-0.01970.08170.0361-0.06940.04380.1656-0.00510.0040.11790.0040.1455-24.0482-30.7914-9.8262
41.3319-0.28290.28430.7479-0.28340.70530.003-0.0180.12640.0371-0.0024-0.0551-0.0670.00730.00810.1312-0.01710.00360.1106-0.0160.1246-7.2468-21.2736-7.9138
51.338-0.2070.79170.6002-0.30911.0881-0.0121-0.1845-0.03070.08590.02690.01410.0239-0.1066-0.02320.135-0.00680.00940.15340.00270.1055-2.1247-11.561124.1717
61.7150.4689-0.22641.3867-0.19250.84640.0461-0.26220.23330.2391-0.040.0254-0.0574-0.0471-0.00160.18130.0114-0.02060.1376-0.04060.19170.186612.055917.959
75.4331-0.42390.29570.3799-0.03140.316-0.05160.07830.3375-0.02890.02520.0799-0.0354-0.06820.0380.1548-0.0003-0.00850.11810.00930.181-6.57194.849211.2266
80.78490.2736-0.04680.8168-0.19490.61920.00540.0151-0.0102-0.02780.0075-0.07110.02010.0173-0.01010.13910.0157-0.00690.1328-0.00870.145210.0413-5.01979.7627
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 72 )A4 - 72
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 226 )A73 - 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 108 )B4 - 108
6X-RAY DIFFRACTION6chain 'B' and (resid 109 through 226 )B109 - 226
7X-RAY DIFFRACTION7chain 'B' and (resid 227 through 282 )B227 - 282
8X-RAY DIFFRACTION8chain 'B' and (resid 283 through 455 )B283 - 455

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