+Open data
-Basic information
Entry | Database: PDB / ID: 6tev | ||||||
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Title | The structure of CYP121 in complex with inhibitor L44 | ||||||
Components | Mycocyclosin synthase | ||||||
Keywords | OXIDOREDUCTASE / CYP121 / Inhibitor / Complex | ||||||
Function / homology | Function and homology information mycocyclosin synthase / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.70001263917 Å | ||||||
Authors | Adam, S. / Koehnke, J. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Chemmedchem / Year: 2021 Title: Structure-Activity Relationship and Mode-Of-Action Studies Highlight 1-(4-Biphenylylmethyl)-1H-imidazole-Derived Small Molecules as Potent CYP121 Inhibitors. Authors: Walter, I. / Adam, S. / Gentilini, M.V. / Kany, A.M. / Brengel, C. / Thomann, A. / Sparwasser, T. / Kohnke, J. / Hartmann, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tev.cif.gz | 289.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tev.ent.gz | 194.9 KB | Display | PDB format |
PDBx/mmJSON format | 6tev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/6tev ftp://data.pdbj.org/pub/pdb/validation_reports/te/6tev | HTTPS FTP |
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-Related structure data
Related structure data | 6te7C 6tetC 1n40S 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 43305.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cyp121, MT2336 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPP6, mycocyclosin synthase | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-HEM / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: Calcium acetate, sodium acetate, PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→47.09 Å / Num. obs: 52925 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 18.4888732536 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.03 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.7→1.79 Å / Num. unique obs: 7523 / CC1/2: 0.891 / Rpim(I) all: 0.227 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N40 Resolution: 1.70001263917→41.5275178694 Å / SU ML: 0.181072114174 / Cross valid method: FREE R-VALUE / σ(F): 1.33626287157 / Phase error: 17.6547622842 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: 26.5468479361 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.70001263917→41.5275178694 Å
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Refine LS restraints |
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LS refinement shell |
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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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