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- PDB-6h1l: Structure of the BM3 heme domain in complex with tioconazole -

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Basic information

Entry
Database: PDB / ID: 6h1l
TitleStructure of the BM3 heme domain in complex with tioconazole
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / P450 / azole inhibitor / heme ligation / P450 BM3
Function / homology
Function and homology information


NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / unspecific monooxygenase / aromatase activity / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / cytosol
Similarity search - Function
Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Cytochrome p450 / Cytochrome P450 / 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. ...Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Cytochrome p450 / Cytochrome P450 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Tioconazole / PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / L(+)-TARTARIC ACID / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.968 Å
AuthorsJeffreys, L.N. / Munro, A.W.M. / Leys, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K001884/1 United Kingdom
CitationJournal: Sci Rep / Year: 2019
Title: Novel insights into P450 BM3 interactions with FDA-approved antifungal azole drugs.
Authors: Jeffreys, L.N. / Poddar, H. / Golovanova, M. / Levy, C.W. / Girvan, H.M. / McLean, K.J. / Voice, M.W. / Leys, D. / Munro, A.W.
History
DepositionJul 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,88222
Polymers104,6232
Non-polymers3,25820
Water9,062503
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A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,11613
Polymers52,3121
Non-polymers1,80512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7659
Polymers52,3121
Non-polymers1,4548
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.980, 150.849, 60.997
Angle α, β, γ (deg.)90.00, 95.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 52311.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: F2Q7T0, unspecific monooxygenase, NADPH-hemoprotein reductase

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Non-polymers , 8 types, 523 molecules

#2: Chemical ChemComp-FJQ / Tioconazole


Mass: 387.711 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13Cl3N2OS / Comment: medication, antifungal*YM
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: PEG, 5mM ligand (dissolved in 100% DMSO), 25mM potassium phosphate, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.968→60.96 Å / Num. obs: 73804 / % possible obs: 98.6 % / Redundancy: 3.4 % / CC1/2: 1 / Rrim(I) all: 0.047 / Net I/σ(I): 15.2
Reflection shellResolution: 1.968→2 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.2 / CC1/2: 0.8 / Rrim(I) all: 0.533 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KF2

4kf2


Resolution: 1.968→60.692 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.52
RfactorNum. reflection% reflection
Rfree0.2149 3631 4.92 %
Rwork0.1894 --
obs0.1907 73804 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.968→60.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7290 0 210 503 8003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057762
X-RAY DIFFRACTIONf_angle_d0.75410501
X-RAY DIFFRACTIONf_dihedral_angle_d14.2324671
X-RAY DIFFRACTIONf_chiral_restr0.0421102
X-RAY DIFFRACTIONf_plane_restr0.0051361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9677-1.99360.30331410.26342664X-RAY DIFFRACTION100
1.9936-2.02090.30491240.25642781X-RAY DIFFRACTION100
2.0209-2.04980.29131240.24892723X-RAY DIFFRACTION100
2.0498-2.08040.27691260.24562731X-RAY DIFFRACTION100
2.0804-2.11290.2781550.23852747X-RAY DIFFRACTION100
2.1129-2.14750.2351270.23022682X-RAY DIFFRACTION100
2.1475-2.18460.29281250.2312809X-RAY DIFFRACTION100
2.1846-2.22430.28691310.23692717X-RAY DIFFRACTION100
2.2243-2.26710.2987830.24542000X-RAY DIFFRACTION72
2.2671-2.31330.2331740.22552681X-RAY DIFFRACTION100
2.3133-2.36360.29761680.22582710X-RAY DIFFRACTION100
2.3636-2.41860.26531370.21942722X-RAY DIFFRACTION100
2.4186-2.47910.30991470.22312722X-RAY DIFFRACTION100
2.4791-2.54620.25671620.21192719X-RAY DIFFRACTION100
2.5462-2.62110.24781430.21742722X-RAY DIFFRACTION100
2.6211-2.70570.24951550.22032735X-RAY DIFFRACTION100
2.7057-2.80240.24521400.21132722X-RAY DIFFRACTION100
2.8024-2.91460.24491360.21492719X-RAY DIFFRACTION100
2.9146-3.04720.2341370.2122725X-RAY DIFFRACTION100
3.0472-3.20790.23111270.20222766X-RAY DIFFRACTION100
3.2079-3.40880.2251400.19782709X-RAY DIFFRACTION99
3.4088-3.6720.19981520.17962715X-RAY DIFFRACTION99
3.672-4.04150.17351310.15812752X-RAY DIFFRACTION99
4.0415-4.62610.17261340.14652737X-RAY DIFFRACTION99
4.6261-5.82770.16991610.15652718X-RAY DIFFRACTION99
5.8277-60.72130.16561510.15592745X-RAY DIFFRACTION99

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