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- PDB-6h1o: Structure of the BM3 heme domain in complex with voriconazole -

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Basic information

Entry
Database: PDB / ID: 6h1o
TitleStructure of the BM3 heme domain in complex with voriconazole
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 / 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 / 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 / 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
PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Voriconazole / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.734 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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)107,46016
Polymers104,6232
Non-polymers2,83714
Water12,881715
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A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,90110
Polymers52,3121
Non-polymers1,5899
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)53,5596
Polymers52,3121
Non-polymers1,2485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.853, 150.009, 61.069
Angle α, β, γ (deg.)90.00, 96.85, 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 / Cytochrome P450(BM-3) / Cytochrome P450BM-3 / Fatty acid monooxygenase / Flavocytochrome P450 BM3


Mass: 52311.621 Da / Num. of mol.: 2 / Mutation: A82F F87V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (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 (E. coli)
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase

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Non-polymers , 6 types, 729 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-VOR / Voriconazole / (2R,3S)-2-(2,4-difluorophenyl)-3-(5-fluoropyrimidin-4-yl)-1-(1H-1,2,4-triazol-1-yl)butan-2-ol


Mass: 349.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14F3N5O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antifungal*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 715 / 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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: PEG, 5mM ligand (dissolved in 100% DMSO), 25mM potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.73→60.633 Å / Num. obs: 99892 / % possible obs: 90.6 % / Redundancy: 3 % / CC1/2: 1 / Rrim(I) all: 0.088 / Net I/σ(I): 8.2
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.2 / CC1/2: 0.9 / Rrim(I) all: 0.383 / % possible all: 93.8

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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: 1.734→60.633 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.03
RfactorNum. reflection% reflection
Rfree0.1997 4831 4.84 %
Rwork0.1611 --
obs0.163 99892 90.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.734→60.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7357 0 189 715 8261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017814
X-RAY DIFFRACTIONf_angle_d1.06810594
X-RAY DIFFRACTIONf_dihedral_angle_d12.6934684
X-RAY DIFFRACTIONf_chiral_restr0.061114
X-RAY DIFFRACTIONf_plane_restr0.0071375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7343-1.7540.25311750.21183279X-RAY DIFFRACTION93
1.754-1.77460.24561560.19133320X-RAY DIFFRACTION95
1.7746-1.79630.251600.18793301X-RAY DIFFRACTION94
1.7963-1.8190.22031420.1813331X-RAY DIFFRACTION95
1.819-1.84290.25331810.18463392X-RAY DIFFRACTION97
1.8429-1.86820.26561610.18553352X-RAY DIFFRACTION96
1.8682-1.89490.21661580.17463432X-RAY DIFFRACTION98
1.8949-1.92320.2031650.19671241X-RAY DIFFRACTION82
1.9232-1.95320.23891500.17352934X-RAY DIFFRACTION87
1.9532-1.98530.19851920.16013354X-RAY DIFFRACTION97
1.9853-2.01950.2071670.16063422X-RAY DIFFRACTION98
2.0195-2.05620.20661820.16053290X-RAY DIFFRACTION94
2.0562-2.09580.2088730.1691572X-RAY DIFFRACTION45
2.0958-2.13850.20011600.16313377X-RAY DIFFRACTION97
2.1385-2.1850.2081510.1663490X-RAY DIFFRACTION98
2.185-2.23590.22281810.16453300X-RAY DIFFRACTION95
2.2359-2.29180.25471390.16322003X-RAY DIFFRACTION59
2.2918-2.35380.18441690.16063441X-RAY DIFFRACTION98
2.3538-2.4230.1971660.16023390X-RAY DIFFRACTION97
2.423-2.50120.1951790.16163388X-RAY DIFFRACTION97
2.5012-2.59060.21451780.17173384X-RAY DIFFRACTION97
2.5906-2.69440.22241690.1693372X-RAY DIFFRACTION96
2.6944-2.8170.1881680.17143376X-RAY DIFFRACTION96
2.817-2.96550.2041800.17283358X-RAY DIFFRACTION96
2.9655-3.15130.20292160.17083315X-RAY DIFFRACTION96
3.1513-3.39460.21711640.16433339X-RAY DIFFRACTION95
3.3946-3.73610.20781280.15433298X-RAY DIFFRACTION93
3.7361-4.27660.16291630.13263346X-RAY DIFFRACTION95
4.2766-5.38760.1631730.14243309X-RAY DIFFRACTION94
5.3876-60.67010.17541850.15643355X-RAY DIFFRACTION95

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