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

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Basic information

Entry
Database: PDB / ID: 7yjf
TitleCrystal structure of the P450 BM3 heme domain mutant F87A/T268P/V78I in complex with N-imidazolyl-pentanoyl-L-phenylalanine and hydroxylamine
ComponentsP450 BM3 heme domain mutant F87A/T268P/V78I
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 / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.515 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

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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)108,9188
Polymers106,9882
Non-polymers1,9306
Water21,7621208
1
A: P450 BM3 heme domain mutant F87A/T268P/V78I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4594
Polymers53,4941
Non-polymers9653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-21 kcal/mol
Surface area17830 Å2
MethodPISA
2
B: P450 BM3 heme domain mutant F87A/T268P/V78I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4594
Polymers53,4941
Non-polymers9653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-20 kcal/mol
Surface area18120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.424, 143.245, 62.062
Angle α, β, γ (deg.)90.000, 97.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein P450 BM3 heme domain mutant F87A/T268P/V78I


Mass: 53493.988 Da / Num. of mol.: 2
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
#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-HOA / HYDROXYAMINE


Mass: 33.030 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H3NO / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1208 / 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: 2.36 Å3/Da / Density % sol: 47.94 %
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: BL10U2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / 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: 1.5→71.62 Å / Num. obs: 258887 / % possible obs: 94.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 17.35 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.058 / Rrim(I) all: 0.105 / Net I/σ(I): 8.4
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
1.52-1.62.70.39355683208780.7670.2980.4972.593.5
4.79-71.623.20.0661460146150.9790.0450.0811593.9

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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: 1.515→39.134 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2027 3644 1.41 %
Rwork0.1682 255243 -
obs0.1687 258887 85.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.55 Å2 / Biso mean: 23.1157 Å2 / Biso min: 5.91 Å2
Refinement stepCycle: final / Resolution: 1.515→39.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7243 0 182 1208 8633
Biso mean--13.93 34.75 -
Num. residues----904
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5154-1.53530.28161200.263925581
1.5353-1.55640.26641370.2551964682
1.5564-1.57860.32181240.2468937882
1.5786-1.60220.29371500.2407960683
1.6022-1.62720.24391210.2294963884
1.6272-1.65390.25191410.2204962484
1.6539-1.68240.26871340.214982484
1.6824-1.7130.29911350.2145973485
1.713-1.74590.25221590.2071987685
1.7459-1.78160.20991410.1964997186
1.7816-1.82030.21651330.1953988786
1.8203-1.86270.21951280.1957993886
1.8627-1.90920.26471490.1996988686
1.9092-1.96090.21381380.1837991186
1.9609-2.01860.21451440.174980385
2.0186-2.08370.18751440.1698996086
2.0837-2.15820.1831390.1651969884
2.1582-2.24460.21651340.1673979785
2.2446-2.34670.20771610.1666968885
2.3467-2.47040.20161300.1697972384
2.4704-2.62520.18621430.1743988286
2.6252-2.82780.23111290.1655982685
2.8278-3.11230.19111470.1586997686
3.1123-3.56240.1751580.13961005987
3.5624-4.48720.15331480.12631033890
4.4872-39.10.18551570.15441031990
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)
11.2440.51591.17490.8980.57762.78490.0276-0.1238-0.0550.1443-0.0298-0.03960.07810.0242-0.0010.16150.00190.00370.15590.02430.13554.6731-15.903827.5809
20.89210.3724-0.27510.9202-0.25250.27530.0197-0.11470.0740.1529-0.0276-0.034-0.07540.01560.00520.1547-0.0096-0.01160.1352-0.00720.13020.7197.444815.0264
31.3061-0.23471.40911.2074-2.13047.1354-0.1773-0.34990.20640.62130.1190.0098-0.8299-0.1680.10410.4440.0457-0.0060.2324-0.05070.2118-7.813713.376325.607
43.9917-0.22780.28830.693-0.09730.6787-0.0920.13190.13860.04220.03820.1312-0.0739-0.10640.04430.1511-0.01790.00050.11010.00870.1299-5.27524.837710.4652
51.03780.4443-0.28310.9797-0.30.9141-0.03840.0525-0.0465-0.03660.0236-0.10130.0430.04050.02380.12440.0019-0.00150.1355-0.01030.12319.8693-7.67798.2779
62.77022.1065-1.90962.5505-2.06074.58370.1078-0.0348-0.06690.0961-0.1318-0.113-0.30190.05740.00550.1360.0278-0.01720.0934-0.02940.147219.36756.90314.1894
71.7006-0.0917-0.91271.1375-0.16192.36890.00070.15270.158-0.0659-0.00190.018-0.10910.0224-0.0080.157-0.00630.00350.15320.03180.1626-15.4958-8.8726-25.7046
81.7431-1.02720.33441.2884-0.42540.52060.0135-0.0007-0.0105-0.03420.0257-0.00420.0417-0.0406-0.0430.1354-0.01850.00250.1312-0.01630.1352-19.7384-31.6101-9.6918
90.5864-0.42970.83052.6806-2.35713.07580.05760.2375-0.0007-0.4164-0.0937-0.03080.16390.19960.00960.26360.0381-0.00660.1999-0.00990.191-18.9921-35.1963-23.6643
101.73340.1212-1.39512.2028-2.3287.9774-0.0580.3109-0.0883-0.5160.0440.1080.4382-0.24450.05340.2965-0.0118-0.04270.173-0.02440.1959-27.6707-38.0091-25.33
114.26350.2967-0.483.82961.77991.98160.0197-0.1864-0.38380.182-0.00380.27910.2191-0.1773-0.04440.135-0.0170.03770.15720.03460.157-36.4713-32.3853-4.4919
120.9277-0.04920.28290.365-0.20440.67250.0559-0.0481-0.02050.0563-0.01370.00630.01010.0395-0.04450.14640.0050.01570.1337-0.01460.1309-11.0761-25.8443-5.9179
132.5521-0.99241.45891.8288-0.54722.0358-0.1063-0.04680.34730.12450.0662-0.0669-0.207-0.00110.05380.1849-0.02040.0370.152-0.00360.225-12.1526-7.2496-13.3017
141.5684-0.89830.91951.207-0.88521.0569-0.0162-0.0946-0.00130.09770.04380.0181-0.021-0.0057-0.03140.15590.00020.00640.1614-0.02230.1253-12.2078-23.9608-4.5387
152.0345-0.77370.87431.8201-1.11142.4360.10220.08630.0428-0.0991-0.1105-0.07080.18210.155700.1604-0.01470.01250.1282-0.03940.15-0.6368-32.0817-13.4868
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 195 )A73 - 195
3X-RAY DIFFRACTION3chain 'A' and (resid 196 through 225 )A196 - 225
4X-RAY DIFFRACTION4chain 'A' and (resid 226 through 282 )A226 - 282
5X-RAY DIFFRACTION5chain 'A' and (resid 283 through 424 )A283 - 424
6X-RAY DIFFRACTION6chain 'A' and (resid 425 through 455 )A425 - 455
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 72 )B4 - 72
8X-RAY DIFFRACTION8chain 'B' and (resid 73 through 158 )B73 - 158
9X-RAY DIFFRACTION9chain 'B' and (resid 159 through 195 )B159 - 195
10X-RAY DIFFRACTION10chain 'B' and (resid 196 through 224 )B196 - 224
11X-RAY DIFFRACTION11chain 'B' and (resid 225 through 250 )B225 - 250
12X-RAY DIFFRACTION12chain 'B' and (resid 251 through 335 )B251 - 335
13X-RAY DIFFRACTION13chain 'B' and (resid 336 through 384 )B336 - 384
14X-RAY DIFFRACTION14chain 'B' and (resid 385 through 424 )B385 - 424
15X-RAY DIFFRACTION15chain 'B' and (resid 425 through 455 )B425 - 455

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