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Yorodumi- PDB-6eic: Crystal structure of Rv0183, a Monoglyceride Lipase from Mycobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eic | ||||||
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Title | Crystal structure of Rv0183, a Monoglyceride Lipase from Mycobacterium Tuberculosis | ||||||
Components | Mycobacterium Tuberculosis Monoglyceride Lipase | ||||||
Keywords | HYDROLASE / Monoglycerid Lipase / Lipase / Alpha/Beta hydrolase | ||||||
Function / homology | Function and homology information symbiont-mediated activation of host apoptosis / glycerolipid catabolic process / acylglycerol lipase / acylglycerol lipase activity / lipase activity / peptidoglycan-based cell wall / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Aschauer, P. / Pavkov-Keller, T. / Oberer, M. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Sci Rep / Year: 2018 Title: The crystal structure of monoacylglycerol lipase from M. tuberculosis reveals the basis for specific inhibition. Authors: Aschauer, P. / Zimmermann, R. / Breinbauer, R. / Pavkov-Keller, T. / Oberer, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eic.cif.gz | 170.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eic.ent.gz | 142.2 KB | Display | PDB format |
PDBx/mmJSON format | 6eic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/6eic ftp://data.pdbj.org/pub/pdb/validation_reports/ei/6eic | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 30298.533 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: Rv0183 / Production host: Escherichia coli (E. coli) / References: UniProt: O07427 #2: Chemical | ChemComp-SO4 / | #3: Chemical | #4: Chemical | ChemComp-NO3 / | #5: 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: 2.33 Å3/Da / Density % sol: 47.32 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 0.03M sodium nitrate, 0.03M di-sodium hydrogenphosphate, 0.03M ammonium sulfate, 0.1M MOPS/HEPES, 12% 2-Methyl 2,4 pentandiol, 12% PEG1000, 12% PEG3350. Microseeding |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97895 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97895 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→49.209 Å / Num. obs: 77304 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.035 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4549 / CC1/2: 0.734 / Rpim(I) all: 0.307 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.209 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→49.209 Å
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Refine LS restraints |
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LS refinement shell |
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