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- PDB-7ydd: Crystal structure of the P450 BM3 heme domain mutant F87A/T268P/V... -

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Basic information

Entry
Database: PDB / ID: 7ydd
TitleCrystal structure of the P450 BM3 heme domain mutant F87A/T268P/V78I in complex with N-imidazolyl-pentanoyl-L-phenylalanine,propylbenzene and hydroxylamine
ComponentsP450 BM3 heme domain mutant F87A/T268P/V78I
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
propylbenzene / 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: 1.663 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: P450 BM3 heme domain mutant F87A/T268P/V78I
B: P450 BM3 heme domain mutant F87A/T268P/V78I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,15810
Polymers106,9882
Non-polymers2,1708
Water17,366964
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A: P450 BM3 heme domain mutant F87A/T268P/V78I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5795
Polymers53,4941
Non-polymers1,0854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-21 kcal/mol
Surface area19200 Å2
MethodPISA
2
B: P450 BM3 heme domain mutant F87A/T268P/V78I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5795
Polymers53,4941
Non-polymers1,0854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-21 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.443, 148.259, 63.899
Angle α, β, γ (deg.)90.000, 99.710, 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 P450 BM3 heme domain mutant F87A/T268P/V78I


Mass: 53493.988 Da / Num. of mol.: 2 / Mutation: V78I,F87A,T268P/
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P14779

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Non-polymers , 5 types, 972 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-3H0 / propylbenzene


Mass: 120.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12 / 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.: 964 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
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: 1.64→74.26 Å / Num. obs: 218554 / % possible obs: 88.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 22.95 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.035 / Rrim(I) all: 0.063 / Net I/σ(I): 11.8
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
1.64-1.733.20.48953509168240.770.3150.5842.387.7
5.18-74.263.30.0351349540980.9960.0230.04226.496.7

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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: 1.663→37.508 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 3546 1.62 %
Rwork0.1561 215008 -
obs0.1567 218554 87.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.48 Å2 / Biso mean: 31.0357 Å2 / Biso min: 10.5 Å2
Refinement stepCycle: final / Resolution: 1.663→37.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7293 0 200 964 8457
Biso mean--29.71 41.32 -
Num. residues----907
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.663-1.68580.34051390.2608879290
1.6858-1.70990.2311460.2444869889
1.7099-1.73540.2771420.2253879889
1.7354-1.76250.261460.2164870289
1.7625-1.79140.26191460.2159858088
1.7914-1.82230.23041460.2008871888
1.8223-1.85540.23571320.1919848988
1.8554-1.89110.20491420.1832855787
1.8911-1.92970.23431490.1742877889
1.9297-1.97170.24321450.1752871590
1.9717-2.01750.23391460.1747879989
2.0175-2.0680.2031380.1671855088
2.068-2.12390.23841420.1591883390
2.1239-2.18640.19481460.1547878290
2.1864-2.25690.18681460.1589880390
2.2569-2.33760.20741480.1602880290
2.3376-2.43120.19861350.1602864889
2.4312-2.54180.18161470.1569871689
2.5418-2.67580.18261420.1598855188
2.6758-2.84340.16591390.1513842186
2.8434-3.06280.18411410.1563837385
3.0628-3.37080.21631340.1449819384
3.3708-3.85820.16081370.1334814784
3.8582-4.85930.17691340.1216822184
4.8593-37.50.15761380.1522834285
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)
11.7784-0.04040.92950.6475-0.22271.3751-0.051-0.1247-0.03670.04450.0650.0730.0027-0.0915-0.01330.1732-0.02250.02210.18980.01320.1515-1.7172-12.141924.4918
21.55010.4956-1.01021.0807-0.79831.20120.0793-0.16620.1480.19610.03420.0997-0.0605-0.0141-0.11470.2725-0.0107-0.02020.1822-0.01820.24390.829812.362318.3558
37.97073.5162-0.12416.94284.32684.0147-0.34120.61450.8292-0.3960.2760.5415-0.43640.1437-0.12350.2568-0.0071-0.11910.33250.12570.3421-18.32545.89826.1112
40.75080.2355-0.02950.9786-0.11170.5068-0.00550.0304-0.0174-0.06470.0083-0.00030.0063-0.0184-0.00270.17750.0012-0.01390.1734-0.00760.15799.1944-3.555510.4266
52.1624-0.2913-1.59351.13580.33094.2358-0.02440.24760.2653-0.03770.0320.0783-0.18960.03490.00150.1671-0.03-0.01760.16650.05220.2053-14.6763-9.1329-26.4109
63.0982-1.82780.64941.5991-0.68950.50610.0012-0.016-0.10220.04820.03070.06140.0217-0.0632-0.03240.1657-0.03390.00730.1336-0.03650.1629-18.8576-32.9557-10.4368
70.7798-1.8832.25477.4617-8.17168.88590.23330.33820.0605-0.7156-0.2366-0.05990.43660.33170.06580.35190.04920.00380.2706-0.03910.2584-18.5906-36.5841-24.7889
83.35190.7979-2.21376.2306-3.42632.8687-0.15840.1829-0.2213-0.55740.05640.06911.5105-0.26480.13070.5343-0.042-0.04310.27-0.06190.3181-27.5565-39.2507-26.3312
97.1592-5.4364-0.43087.79375.17036.4615-0.2405-0.1439-0.90120.43350.09020.53370.6430.04170.010.2467-0.07780.11920.28850.05080.3348-36.4629-33.2746-5.0457
102.22190.66441.3050.82230.37470.7781-0.1077-0.0245-0.21070.06810.06920.1228-0.013-0.05970.00840.2264-0.00540.03280.17450.00110.1914-16.6158-30.3939-13.8388
111.3215-0.37970.56340.9797-0.62381.0525-0.0485-0.01170.16930.12420.0084-0.0261-0.14880.00880.04910.1967-0.01760.00970.1656-0.030.1654-9.1677-19.0154-7.0538
122.5731-2.34552.40344.3379-3.26825.76450.13890.1583-0.0444-0.2885-0.07830.01110.24620.0401-0.0270.1352-0.05030.01780.1349-0.05270.15460.6053-33.4486-14.4626
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 225 )A109 - 225
3X-RAY DIFFRACTION3chain 'A' and (resid 226 through 250 )A226 - 250
4X-RAY DIFFRACTION4chain 'A' and (resid 251 through 456 )A251 - 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 195 )B159 - 195
8X-RAY DIFFRACTION8chain 'B' and (resid 196 through 224 )B196 - 224
9X-RAY DIFFRACTION9chain 'B' and (resid 225 through 250 )B225 - 250
10X-RAY DIFFRACTION10chain 'B' and (resid 251 through 282 )B251 - 282
11X-RAY DIFFRACTION11chain 'B' and (resid 283 through 424 )B283 - 424
12X-RAY DIFFRACTION12chain 'B' and (resid 425 through 455 )B425 - 455

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