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- PDB-7qke: Crystal structure of CYP125 from Mycobacterium tuberculosis in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qke | ||||||
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Title | Crystal structure of CYP125 from Mycobacterium tuberculosis in complex with inhibitor (surface entropy reduction mutant) | ||||||
![]() | Steroid C26-monooxygenase | ||||||
![]() | OXIDOREDUCTASE / P450 / CYP / Tuberculosis / cholesterol / inhibitor / complex / surface / entropy / reduction / cytochrome | ||||||
Function / homology | ![]() cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming] / biological process involved in interaction with host / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Snee, M. / Tunnicliffe, R. / Leys, D. / Levy, C. / Katariya, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure Based Discovery of Inhibitors of CYP125 and CYP142 from Mycobacterium tuberculosis. Authors: Katariya, M.M. / Snee, M. / Tunnicliffe, R.B. / Kavanagh, M.E. / Boshoff, H.I.M. / Amadi, C.N. / Levy, C.W. / Munro, A.W. / Abell, C. / Leys, D. / Coyne, A.G. / McLean, K.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 303.3 KB | Display | ![]() |
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PDB format | ![]() | 205.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 961.1 KB | Display | ![]() |
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Full document | ![]() | 962.9 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qjlC ![]() 7qnnC ![]() 7qwnC ![]() 7r1iC ![]() 7r3uC ![]() 7yxfC ![]() 7zlzC ![]() 7zqrC ![]() 7zsuC ![]() 7zt0C ![]() 7zxdC ![]() 3iw0S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 46489.078 Da / Num. of mol.: 1 / Mutation: K153A, K332A, K333A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: cyp125, cyp125A1, Rv3545c, MTCY03C7.11 / Plasmid: Pet21a / Production host: ![]() ![]() References: UniProt: P9WPP1, cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming] |
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#2: Chemical | ChemComp-E1V / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.38 % / Description: Plate like, very thin |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 22% PEG8000, 0.1M sodium cacodylate pH 5.0, 0.2M sodium acetate trihydrate Temp details: 4C |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→49.22 Å / Num. obs: 21451 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 47.66 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.046 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.202 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2058 / CC1/2: 0.924 / Rpim(I) all: 0.355 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3IW0 Resolution: 2.3→37.7 Å / SU ML: 0.3126 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.458 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→37.7 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 6.64673395583 Å / Origin y: 20.1590852159 Å / Origin z: 17.9485208234 Å
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Refinement TLS group | Selection details: all |