+Open data
-Basic information
Entry | Database: PDB / ID: 6h1s | ||||||
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Title | Structure of the BM3 heme domain in complex with fluconazole | ||||||
Components | Bifunctional cytochrome P450/NADPH--P450 reductase | ||||||
Keywords | OXIDOREDUCTASE / 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 / metabolic process / FMN binding / iron ion binding / heme binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus megaterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Jeffreys, L.N. / Munro, A.W.M. / Leys, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h1s.cif.gz | 212.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h1s.ent.gz | 169.3 KB | Display | PDB format |
PDBx/mmJSON format | 6h1s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/6h1s ftp://data.pdbj.org/pub/pdb/validation_reports/h1/6h1s | HTTPS FTP |
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-Related structure data
Related structure data | 6h1lC 6h1oC 6h1tC 4kf2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 0
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | 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 , 5 types, 579 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: PEG, 5mM ligand (dissolved in 100% DMSO), 25mM potassium phosphate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→119.29 Å / Num. obs: 74443 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 1 / Rrim(I) all: 0.113 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.95→1.99 Å / Redundancy: 6.1 % / CC1/2: 0.8 / Rrim(I) all: 0.815 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KF2 Resolution: 1.95→73.35 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.507 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.523 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→73.35 Å
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Refine LS restraints |
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