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- PDB-7y0s: Crystal structure of the P450 BM3 heme domain mutant F87A in comp... -

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Basic information

Entry
Database: PDB / ID: 7y0s
TitleCrystal structure of the P450 BM3 heme domain mutant F87A in complex with N-imidazolyl-hexanoyl-L-tyrosyl-L-tyrosine and hydroxylamine
Components
  • Bifunctional cytochrome P450/NADPH--P450 reductase
  • I7X-TYR-TYR
KeywordsOXIDOREDUCTASE / Dual-functional small molecule / P450 heme domain / Complex
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 / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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 F87A in complex with N-imidazolyl-hexanoyl-L-tyrosyl-L-tyrosine 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Bifunctional cytochrome P450/NADPH--P450 reductase
A: Bifunctional cytochrome P450/NADPH--P450 reductase
C: I7X-TYR-TYR
D: I7X-TYR-TYR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,0228
Polymers107,7234
Non-polymers1,2994
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-57 kcal/mol
Surface area32290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.432, 143.775, 63.043
Angle α, β, γ (deg.)90.000, 99.830, 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: 53352.758 Da / Num. of mol.: 2 / Mutation: F87A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
Strain: ATCC 14581 / DSM 32 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / VKM B-512
Gene: cyp102A1, cyp102, BG04_163 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Protein/peptide I7X-TYR-TYR


Mass: 508.568 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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-HOA / HYDROXYAMINE


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


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 48.34 %
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: BL10U2 / Wavelength: 0.97914 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: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.06→71.89 Å / Num. obs: 59965 / % possible obs: 97.1 % / Redundancy: 2.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.054 / Rrim(I) all: 0.09 / Net I/σ(I): 9 / Num. measured all: 146021
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
2.06-2.182.50.4962221388830.7620.3640.6192.498.8
6.53-71.892.30.03453519690.9960.0240.03819.898.3

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Processing

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

7egn


Resolution: 2.06→52.66 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 2000 3.34 %
Rwork0.2233 57918 -
obs0.2234 59918 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.25 Å2 / Biso mean: 39.6456 Å2 / Biso min: 16.52 Å2
Refinement stepCycle: final / Resolution: 2.06→52.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6896 0 164 440 7500
Biso mean--33.85 41.61 -
Num. residues----882
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.06-2.120.30491450.29434216436199
2.12-2.170.32171450.27194197434299
2.17-2.240.2741440.26854169431398
2.24-2.310.29111450.25984190433598
2.31-2.390.24291430.25524144428797
2.39-2.490.26221430.24874140428398
2.49-2.60.2321430.24564143428697
2.6-2.740.22411430.24064127427096
2.74-2.910.21581380.23344028416695
2.91-3.130.24561420.23874110425296
3.13-3.450.21581390.2224037417695
3.45-3.950.23351410.20534054419595
3.95-4.970.17441430.18634117426096
4.97-52.660.22471460.2074246439298

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