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- PDB-7rtq: Sterol 14alpha demethylase (CYP51) from Naegleria fowleri in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rtq | ||||||
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Title | Sterol 14alpha demethylase (CYP51) from Naegleria fowleri in complex with an inhibitor R)-N-(1-(3,4'-difluorobiphenyl-4-yl)-2-(1H-imidazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxadiazol-2-yl)benzamide | ||||||
![]() | Protein CYP51 | ||||||
![]() | OXIDOREDUCTASE / CYTOCHROME P450 / CYP51 / sterol 14 alpha- demethylase | ||||||
Function / homology | ![]() steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / bile acid biosynthetic process / cholesterol homeostasis / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lepesheva, G.I. / Hargrove, T.Y. / Wawrzak, Z. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Relaxed Substrate Requirements of Sterol 14 alpha-Demethylase from Naegleria fowleri Are Accompanied by Resistance to Inhibition. Authors: Hargrove, T.Y. / Wawrzak, Z. / Rachakonda, G. / Nes, W.D. / Villalta, F. / Guengerich, F.P. / Lepesheva, G.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 775.7 KB | Display | ![]() |
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PDB format | ![]() | 646.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.6 MB | Display | ![]() |
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Full document | ![]() | 3.7 MB | Display | |
Data in XML | ![]() | 76.9 KB | Display | |
Data in CIF | ![]() | 106.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3g1qS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 35 - 483 / Label seq-ID: 10 - 458
NCS ensembles :
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Components
#1: Protein | Mass: 53559.992 Da / Num. of mol.: 4 / Fragment: 6 His tag added to the C-terminus / Mutation: N33K, E34L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: NF0102700 / Production host: ![]() ![]() #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-7PW / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.34 mM n-Dodecyl-beta-D-maltoside, 5.54 mM TCEP, 15% PEG 3350 (w/v), 5% isopropanol , 0.1M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 22, 2021 / Details: Be lens |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→67.08 Å / Num. obs: 113996 / % possible obs: 96.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 23.3 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.073 / Rrim(I) all: 0.099 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.11→2.2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 16740 / CC1/2: 0.778 / Rpim(I) all: 0.339 / Rrim(I) all: 0.613 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3g1q Resolution: 2.11→64.63 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.916 / SU B: 13.738 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 126.85 Å2 / Biso mean: 28.549 Å2 / Biso min: 8.16 Å2
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Refinement step | Cycle: final / Resolution: 2.11→64.63 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.11→2.165 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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