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

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Basic information

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


NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / unspecific monooxygenase / aromatase activity / 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 / 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
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: 2.01 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
Revision 1.2Nov 13, 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

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-Tyr-Tyr
D: Im-C6-Tyr-Tyr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9566
Polymers107,7234
Non-polymers1,2332
Water13,079726
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)58.673, 148.281, 64.703
Angle α, β, γ (deg.)90.00, 99.90, 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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 726 / 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: 2.57 Å3/Da / Density % sol: 52.21 %
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: 2.01→74.14 Å / Num. obs: 66199 / % possible obs: 91.6 % / Redundancy: 2.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.048 / Rrim(I) all: 0.08 / Χ2: 0.41 / Net I/σ(I): 7.6 / Num. measured all: 166536
Reflection shellResolution: 2.01→2.12 Å / % possible obs: 94.8 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.369 / Num. measured all: 25375 / Num. unique obs: 9974 / CC1/2: 0.727 / Rpim(I) all: 0.282 / Rrim(I) all: 0.467 / Χ2: 0.35 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
Aimlessdata scaling
autoPROCdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→39.71 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2055 4965 7.54 %
Rwork0.1792 --
obs0.1812 65817 90.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→39.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7168 0 86 726 7980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087448
X-RAY DIFFRACTIONf_angle_d0.97810113
X-RAY DIFFRACTIONf_dihedral_angle_d19.0432743
X-RAY DIFFRACTIONf_chiral_restr0.2151085
X-RAY DIFFRACTIONf_plane_restr0.0061311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.030.24411680.23542087X-RAY DIFFRACTION92
2.03-2.050.27281590.23362018X-RAY DIFFRACTION92
2.05-2.080.29981650.22022055X-RAY DIFFRACTION92
2.08-2.110.27141680.2242058X-RAY DIFFRACTION92
2.11-2.130.24411670.22012040X-RAY DIFFRACTION93
2.13-2.160.27891740.21412107X-RAY DIFFRACTION93
2.16-2.190.2831710.21712079X-RAY DIFFRACTION94
2.19-2.230.25491680.22062062X-RAY DIFFRACTION93
2.23-2.260.27571720.22892099X-RAY DIFFRACTION94
2.26-2.30.29221700.21572088X-RAY DIFFRACTION94
2.3-2.340.24021720.19892106X-RAY DIFFRACTION94
2.34-2.380.19031700.19162071X-RAY DIFFRACTION93
2.38-2.430.25241690.18552076X-RAY DIFFRACTION93
2.43-2.480.24321700.19392064X-RAY DIFFRACTION93
2.48-2.530.23261670.22049X-RAY DIFFRACTION93
2.53-2.590.23951680.18462049X-RAY DIFFRACTION91
2.59-2.650.19951700.18782078X-RAY DIFFRACTION93
2.65-2.720.22471630.18571997X-RAY DIFFRACTION91
2.72-2.80.20221690.17682064X-RAY DIFFRACTION91
2.8-2.90.22311650.18052022X-RAY DIFFRACTION91
2.9-30.20311630.18282000X-RAY DIFFRACTION90
3-3.120.22431680.18682037X-RAY DIFFRACTION90
3.12-3.260.20431630.17742005X-RAY DIFFRACTION89
3.26-3.430.19561610.171967X-RAY DIFFRACTION88
3.43-3.650.20431600.16881954X-RAY DIFFRACTION88
3.65-3.930.18931580.1561942X-RAY DIFFRACTION87
3.93-4.320.14731560.14581900X-RAY DIFFRACTION85
4.32-4.950.13971590.14461954X-RAY DIFFRACTION86
4.95-6.230.20711560.17471921X-RAY DIFFRACTION86
6.23-39.710.15221560.16791903X-RAY DIFFRACTION83

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