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- PDB-7ydl: Crystal structure of the P450 BM3 heme domain mutant F87A/T268I/A... -

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Basic information

Entry
Database: PDB / ID: 7ydl
TitleCrystal structure of the P450 BM3 heme domain mutant F87A/T268I/A184V/A82T in complex with N-imidazolyl-hexanoyl-L-phenylalanine
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 / 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: 1.58 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: To Be Published
Title: Crystal structure of the P450 BM3 heme domain mutant F87A/T268I/A184V/A82T in complex with N-imidazolyl-hexanoyl-L-phenylalanine
Authors: Dong, S. / Chen, J. / Jiang, Y. / Cong, Z. / Feng, Y.
History
DepositionJul 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 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)109,0006
Polymers107,1082
Non-polymers1,8924
Water20,3031127
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5003
Polymers53,5541
Non-polymers9462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-21 kcal/mol
Surface area19030 Å2
MethodPISA
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5003
Polymers53,5541
Non-polymers9462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-21 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.410, 148.040, 64.120
Angle α, β, γ (deg.)90.000, 100.100, 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: 53554.086 Da / Num. of mol.: 2 / Mutation: A82T,F87A,A184V,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
#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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1127 / 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: 51.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M magnesium formate dihydrate, 0.2 M Magnesium chloride hexahydrate, 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.58→37.92 Å / Num. obs: 270943 / % possible obs: 98.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 23.66 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.031 / Rrim(I) all: 0.057 / Net I/σ(I): 13.4
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
1.58-1.623.40.55437007107730.7620.3480.6562.199.9
7.07-37.923.20.029515016270.9970.0190.03431.996.7

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1fag

1fag


Resolution: 1.58→37.01 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2002 7161 4.98 %
Rwork0.1771 257459 -
obs0.1783 270943 93.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.12 Å2 / Biso mean: 31.882 Å2 / Biso min: 15.29 Å2
Refinement stepCycle: final / Resolution: 1.58→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7295 0 134 1127 8556
Biso mean--31.01 42.73 -
Num. residues----905
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.58-1.5980.33764960.2888879797
1.598-1.61680.29814790.2767885596
1.6168-1.63650.29014740.2656880696
1.6365-1.65720.31554750.2664880996
1.6572-1.6790.2955110.2634876495
1.679-1.7020.25694960.2426881897
1.702-1.72630.25994510.2361889597
1.7263-1.75210.27414560.2336895297
1.7521-1.77950.24034480.2277888897
1.7795-1.80860.21714670.2121879596
1.8086-1.83980.23514510.1997881796
1.8398-1.87330.21294340.2041886695
1.8733-1.90930.22134130.1928855494
1.9093-1.94830.23074920.1978881595
1.9483-1.99060.25344010.1987873496
1.9906-2.03690.21864390.1935873195
2.0369-2.08790.18434120.1857869194
2.0879-2.14430.20774730.1873854893
2.1443-2.20740.18654160.1765847092
2.2074-2.27860.21224180.1848845092
2.2786-2.36010.23025060.1792829292
2.3601-2.45450.21334170.1841838791
2.4545-2.56620.1924180.1788834790
2.5662-2.70150.18944470.1814818589
2.7015-2.87070.20914120.1826821089
2.8707-3.09220.21554400.1785819489
3.0922-3.40320.18994680.1593809489
3.4032-3.89520.17314180.1486808288
3.8952-4.90570.15114260.1338833990
4.9057-370.17144300.1656827490
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)
11.06310.06960.72240.68670.04511.4270.0406-0.2401-0.11280.1143-0.03130.05650.1111-0.1033-0.00090.2394-0.02240.00020.26470.01780.2208-20.2554-16.4307-2.7659
21.24560.56470.09331.5241-0.16170.50340.0381-0.18120.16080.2303-0.04750.0148-0.1296-0.08540.0090.2270.0292-0.01140.2139-0.03550.2076-26.35899.0928-13.6809
32.0017-0.0951-0.00590.44580.02390.4036-0.0259-0.06480.1493-0.00240.0170.0877-0.0478-0.08710.01210.22970.0043-0.01060.19350.00630.2314-30.30055.1897-20.2623
40.79770.2083-0.04461.0203-0.22870.82090.02110.048-0.0281-0.0883-0.0067-0.05650.0460.0179-0.01190.16720.0263-0.00130.1736-0.00520.181-13.3112-4.8302-21.6756
51.19-0.1662-0.50240.591-0.29531.45150.03820.29360.2196-0.0463-0.06450.0361-0.13210.00280.02560.26630.00240.0190.27690.04170.2979-38.2932-9.0836-57.8253
61.8548-0.93630.08541.261-0.15850.32660.10060.0627-0.1097-0.0483-0.0630.03460.0371-0.0326-0.03660.1986-0.0170.00230.1826-0.02660.1957-42.3822-32.7537-41.7813
71.2008-0.2472-0.24331.1262-0.08361.61250.11570.4368-0.2263-0.4856-0.17850.14870.0722-0.1672-0.00310.36210.0209-0.01470.3365-0.11640.3087-46.8002-37.5232-56.8218
82.0965-0.2302-0.22360.3970.25930.56480.02740.0032-0.25660.0394-0.0540.12760.0805-0.09530.02810.2289-0.01730.00910.18960.00770.2314-48.0793-31.2622-41.615
91.182-0.34160.29250.7599-0.40350.98040.0157-0.06830.14120.13270.010.0216-0.16930.0182-0.0110.1984-0.03040.01130.1778-0.03310.1928-32.9032-18.865-38.4454
101.8707-0.45940.34231.39020.00991.43280.139-0.0979-0.1887-0.0677-0.0164-0.01180.12280.0051-0.08930.2179-0.01970.00460.2576-0.00210.248-22.8385-33.194-46.0133
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 72 )A3 - 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 72 )B4 - 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 455 )B425 - 455

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