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- PDB-7y0r: Crystal structure of the P450 BM3 heme domain mutant F87L/V78S/A1... -

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Basic information

Entry
Database: PDB / ID: 7y0r
TitleCrystal structure of the P450 BM3 heme domain mutant F87L/V78S/A184V in complex with N-imidazolyl-hexanoyl-L-phenylalanine, p-toluidine and hydroxylamine
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / Dual-functional small molecule / P450 heme domain / Complex
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 / FMN binding / iron ion binding / heme binding / identical protein binding / cytoplasm
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
4-METHYLANILINE / PROTOPORPHYRIN IX CONTAINING FE / HYDROXYAMINE / 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: 2.09 Å
AuthorsJiang, Y. / Dong, S. / Feng, Y. / Cong, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21778060 China
National Natural Science Foundation of China (NSFC)21977104 China
CitationJournal: To Be Published
Title: Crystal structure of the P450 BM3 heme domain mutant F87L/V78S/A184V in complex with N-imidazolyl-hexanoyl-L-phenylalanine, p-toluidine and hydroxylamine
Authors: Jiang, Y. / Dong, S. / Feng, Y. / Cong, Z.
History
DepositionJun 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 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)109,65312
Polymers106,8222
Non-polymers2,83110
Water10,755597
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-43 kcal/mol
Surface area35350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.034, 149.907, 65.763
Angle α, β, γ (deg.)90.000, 100.580, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 108 or (resid 109...
21(chain B and (resid 3 through 109 or (resid 110...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSSERSER(chain A and (resid 3 through 108 or (resid 109...AA3 - 1085 - 110
12GLNGLNALAALA(chain A and (resid 3 through 108 or (resid 109...AA109 - 111111 - 113
13LYSLYSLEULEU(chain A and (resid 3 through 108 or (resid 109...AA3 - 4555 - 457
14LYSLYSLEULEU(chain A and (resid 3 through 108 or (resid 109...AA3 - 4555 - 457
15LYSLYSLEULEU(chain A and (resid 3 through 108 or (resid 109...AA3 - 4555 - 457
16LYSLYSLEULEU(chain A and (resid 3 through 108 or (resid 109...AA3 - 4555 - 457
21LYSLYSGLNGLN(chain B and (resid 3 through 109 or (resid 110...BB3 - 1095 - 111
22GLNGLNALAALA(chain B and (resid 3 through 109 or (resid 110...BB110 - 111112 - 113
23LYSLYSLEULEU(chain B and (resid 3 through 109 or (resid 110...BB3 - 4555 - 457
24LYSLYSLEULEU(chain B and (resid 3 through 109 or (resid 110...BB3 - 4555 - 457
25LYSLYSLEULEU(chain B and (resid 3 through 109 or (resid 110...BB3 - 4555 - 457
26LYSLYSLEULEU(chain B and (resid 3 through 109 or (resid 110...BB3 - 4555 - 457

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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: 53410.836 Da / Num. of mol.: 2 / Mutation: V78S, F87L, A184V
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, 607 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HOA / HYDROXYAMINE / Hydroxylamine


Mass: 33.030 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H3NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-IC6 / (2S)-2-(6-imidazol-1-ylhexanoylamino)-3-phenyl-propanoic acid


Mass: 329.394 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H23N3O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-4MN / 4-METHYLANILINE / Toluidine


Mass: 107.153 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9N / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 597 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.38M MgCl2, 0.1M Tris 8.5, 12-18% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97914 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.09→74.95 Å / Num. obs: 65192 / % possible obs: 98.3 % / Redundancy: 3.4 % / CC1/2: 0.971 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.109 / Rrim(I) all: 0.203 / Net I/σ(I): 5.2
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
2.09-2.20.6573504597190.6850.4060.7752.499.8
6.6-74.950.114754321190.9780.070.1348.798.4

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EGN

7egn


Resolution: 2.09→39.71 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2411 3786 3.06 %
Rwork0.2137 119789 -
obs0.2145 65178 93.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.78 Å2 / Biso mean: 31.5262 Å2 / Biso min: 11.35 Å2
Refinement stepCycle: final / Resolution: 2.09→39.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7095 0 202 597 7894
Biso mean--23.8 36.65 -
Num. residues----903
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2748X-RAY DIFFRACTION4.868TORSIONAL
12B2748X-RAY DIFFRACTION4.868TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.09-2.110.37641460.3064637478398
2.11-2.140.3291430.28964608475197
2.14-2.170.38471480.2954658480697
2.17-2.20.27421450.28464565471097
2.2-2.230.36691440.28644552469697
2.23-2.270.29341480.27524625477396
2.27-2.310.30331410.27774395453695
2.31-2.350.30911450.26794618476395
2.35-2.390.27451390.26414382452195
2.39-2.430.2471450.25784588473395
2.43-2.480.25021420.25344395453794
2.48-2.540.30021360.24424461459794
2.54-2.60.28771340.24124380451493
2.6-2.660.29181400.24514400454093
2.66-2.730.2631330.24934387452092
2.73-2.810.26121400.23314355449592
2.81-2.90.30951400.22844336447692
2.9-3.010.2441370.23364367450492
3.01-3.130.2621350.22614290442590
3.13-3.270.20511380.21194317445591
3.27-3.440.26051420.20814275441791
3.44-3.660.18251390.18184305444491
3.66-3.940.21011340.17784267440190
3.94-4.340.17881300.16494255438590
4.34-4.960.20231400.1564426456693
4.96-6.250.20111400.18564415455594
6.25-39.710.18281420.17394530467295
Refinement TLS params.Method: refined / Origin x: -4.862 Å / Origin y: -12.0841 Å / Origin z: 0.3528 Å
111213212223313233
T0.0701 Å2-0.0033 Å20.0084 Å2-0.0855 Å2-0.0067 Å2--0.0777 Å2
L0.0846 °20.1111 °20.09 °2-0.2344 °20.1404 °2--0.1216 °2
S-0.0089 Å °0.0129 Å °-0.0108 Å °0.0027 Å °0.0212 Å °-0.0238 Å °-0.0049 Å °-0.0012 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 455
2X-RAY DIFFRACTION1allA501 - 901
3X-RAY DIFFRACTION1allB3 - 455
4X-RAY DIFFRACTION1allB501 - 901
5X-RAY DIFFRACTION1allS1 - 597

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