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Yorodumi- PDB-7qq7: Crystal structure of CYP142 from Mycobacterium tuberculosis in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qq7 | ||||||
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Title | Crystal structure of CYP142 from Mycobacterium tuberculosis in complex with an inhibitor at partial occupancy with PEG | ||||||
Components | Steroid C26-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / CYP / Cytochrome / P450 / Inhibitor / tuberculosis / cholesterol / monooxygenase | ||||||
Function / homology | Function and homology information cholesterol 26-hydroxylase activity / cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / peptidoglycan-based cell wall / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Snee, M. / Levy, C. / Kavanagh, M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Crystal structure of CYP142 from Mycobacterium tuberculosis in complex with an inhibitor at partial occupancy with PEG Authors: Kavanagh, M. / Snee, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qq7.cif.gz | 196 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qq7.ent.gz | 144.1 KB | Display | PDB format |
PDBx/mmJSON format | 7qq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qq7_validation.pdf.gz | 1016 KB | Display | wwPDB validaton report |
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Full document | 7qq7_full_validation.pdf.gz | 1017.3 KB | Display | |
Data in XML | 7qq7_validation.xml.gz | 22 KB | Display | |
Data in CIF | 7qq7_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/7qq7 ftp://data.pdbj.org/pub/pdb/validation_reports/qq/7qq7 | HTTPS FTP |
-Related structure data
Related structure data | 2xkrS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44371.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: cyp142, cyp142A1, Rv3518c, MTV023.25c / Details (production host): Pet21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 References: UniProt: P9WPL5, cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] |
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-Non-polymers , 7 types, 473 molecules
#2: Chemical | ChemComp-HEM / | ||||||
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#3: Chemical | ChemComp-ACT / | ||||||
#4: Chemical | ChemComp-PG4 / | ||||||
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-EIQ / ~{ | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.62 Å3/Da / Density % sol: 53.02 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 8% PEG 20000, 8% PEG 550MME, 0.1M sodium acetate pH4.5, 0.2M KBr Temp details: 4C |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: N2 cryostream / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→55.31 Å / Num. obs: 62174 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 20.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.041 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3085 / CC1/2: 0.841 / Rrim(I) all: 0.864 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XKR Resolution: 1.6→50.8 Å / SU ML: 0.1567 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.4135 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: 25.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→50.8 Å
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Refine LS restraints |
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LS refinement shell |
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