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- PDB-8hos: Crystal structure of the P450 BM3 heme domain mutant F87A in comp... -

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Basic information

Entry
Database: PDB / ID: 8hos
TitleCrystal structure of the P450 BM3 heme domain mutant F87A in complex with Im-C6-Phe(4NO2)-Tyr
Components
  • Bifunctional cytochrome P450/NADPH--P450 reductase
  • Im-C6-Phe(4NO2)-Tyr
KeywordsOXIDOREDUCTASE / Dual-functional small molecule / P450 heme domain
Function / homology
Function and homology information


aromatase activity / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / unspecific monooxygenase / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme 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 / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsJiang, Y. / Dong, S. / Feng, Y. / Cong, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22207112 China
National Natural Science Foundation of China (NSFC)21977104 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Anchoring a Structurally Editable Proximal Cofactor-like Module to Construct an Artificial Dual-center Peroxygenase.
Authors: Qin, X. / Jiang, Y. / Yao, F. / Chen, J. / Kong, F. / Zhao, P. / Jin, L. / Cong, Z.
History
DepositionDec 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional cytochrome P450/NADPH--P450 reductase
B: Bifunctional cytochrome P450/NADPH--P450 reductase
C: Im-C6-Phe(4NO2)-Tyr
D: Im-C6-Phe(4NO2)-Tyr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,0146
Polymers107,7814
Non-polymers1,2332
Water14,016778
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.436, 147.341, 64.260
Angle α, β, γ (deg.)90.00, 99.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bifunctional cytochrome P450/NADPH--P450 reductase


Mass: 53352.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (bacteria) / Gene: BTA37_15100 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A1Q8UP87, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Protein/peptide Im-C6-Phe(4NO2)-Tyr


Mass: 537.566 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 778 / 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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / 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: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.82→73.67 Å / Num. obs: 94570 / % possible obs: 98.8 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.038 / Rrim(I) all: 0.07 / Χ2: 0.88 / Net I/σ(I): 10.3 / Num. measured all: 308700
Reflection shellResolution: 1.82→1.92 Å / % possible obs: 99.2 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.389 / Num. measured all: 40667 / Num. unique obs: 13817 / CC1/2: 0.864 / Rpim(I) all: 0.263 / Rrim(I) all: 0.471 / Χ2: 0.64 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
Aimlessdata scaling
autoPROCdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→46.72 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2092 6000 6.35 %
Rwork0.1805 --
obs0.1824 94494 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7162 0 86 778 8026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047435
X-RAY DIFFRACTIONf_angle_d0.76510096
X-RAY DIFFRACTIONf_dihedral_angle_d19.2722726
X-RAY DIFFRACTIONf_chiral_restr0.1631086
X-RAY DIFFRACTIONf_plane_restr0.0051308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.840.31872010.26472965X-RAY DIFFRACTION99
1.84-1.860.28811990.25422926X-RAY DIFFRACTION99
1.86-1.880.27652030.25172997X-RAY DIFFRACTION99
1.88-1.910.2721960.23962887X-RAY DIFFRACTION99
1.91-1.930.26452010.25212960X-RAY DIFFRACTION98
1.93-1.960.27682010.23262959X-RAY DIFFRACTION99
1.96-1.990.26221990.20562946X-RAY DIFFRACTION100
1.99-2.020.23152040.18953000X-RAY DIFFRACTION100
2.02-2.050.23181990.19172944X-RAY DIFFRACTION100
2.05-2.080.23842070.18823035X-RAY DIFFRACTION100
2.08-2.120.23851970.19822926X-RAY DIFFRACTION100
2.12-2.160.24742040.19532997X-RAY DIFFRACTION100
2.16-2.20.24622020.19043001X-RAY DIFFRACTION100
2.2-2.240.25992010.19862951X-RAY DIFFRACTION100
2.24-2.290.24752030.19632983X-RAY DIFFRACTION100
2.29-2.350.21312000.18912959X-RAY DIFFRACTION100
2.35-2.40.21432020.18612981X-RAY DIFFRACTION99
2.4-2.470.19732020.18962979X-RAY DIFFRACTION99
2.47-2.540.21951990.19172953X-RAY DIFFRACTION99
2.54-2.620.22371980.19012909X-RAY DIFFRACTION98
2.62-2.720.23521990.20212942X-RAY DIFFRACTION99
2.72-2.830.21472020.19212970X-RAY DIFFRACTION99
2.83-2.960.24011980.19472935X-RAY DIFFRACTION98
2.96-3.110.23341980.19522924X-RAY DIFFRACTION98
3.11-3.310.19891980.182909X-RAY DIFFRACTION97
3.31-3.560.19221980.1732922X-RAY DIFFRACTION97
3.56-3.920.18491940.1632865X-RAY DIFFRACTION96
3.92-4.490.16431960.14142893X-RAY DIFFRACTION96
4.49-5.650.16181970.14942902X-RAY DIFFRACTION97
5.65-46.720.19732020.16652974X-RAY DIFFRACTION98

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