+Open data
-Basic information
Entry | Database: PDB / ID: 7p0y | |||||||||
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Title | Crystal Structure of mtbMGL K74A (Substrate Analog Complex) | |||||||||
Components | Monoacylglycerol lipase | |||||||||
Keywords | HYDROLASE / Mycobacterium tuberculosis / monoacylglycerol lipase | |||||||||
Function / homology | Function and homology information symbiont-mediated activation of host apoptosis / acylglycerol lipase / glycerolipid catabolic process / monoacylglycerol lipase activity / lipase activity / peptidoglycan-based cell wall / extracellular region / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Grininger, C. / Aschauer, P. / Pavkov-Keller, T. / Oberer, M. | |||||||||
Funding support | Austria, 2items
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Citation | Journal: Biomolecules / Year: 2021 Title: Structural Changes in the Cap of Rv0183/mtbMGL Modulate the Shape of the Binding Pocket. Authors: Grininger, C. / Leypold, M. / Aschauer, P. / Pavkov-Keller, T. / Riegler-Berket, L. / Breinbauer, R. / Oberer, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p0y.cif.gz | 131.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p0y.ent.gz | 93.1 KB | Display | PDB format |
PDBx/mmJSON format | 7p0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p0y_validation.pdf.gz | 725.5 KB | Display | wwPDB validaton report |
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Full document | 7p0y_full_validation.pdf.gz | 736 KB | Display | |
Data in XML | 7p0y_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 7p0y_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/7p0y ftp://data.pdbj.org/pub/pdb/validation_reports/p0/7p0y | HTTPS FTP |
-Related structure data
Related structure data | 7ozmC 6eicS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30643.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: Rv0183, LH57_01015 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O07427, acylglycerol lipase #2: Chemical | #3: Water | ChemComp-HOH / | 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: 2.36 Å3/Da / Density % sol: 47.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30 % PEG300, 125 mM Calcium acetate, 100 mM Tris-HCl pH 8.5, 10 mg/ml protein |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→40.78 Å / Num. obs: 28192 / % possible obs: 99.65 % / Redundancy: 5.2 % / Biso Wilson estimate: 36.18 Å2 / CC1/2: 0.99 / CC star: 0.998 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.071 / Rrim(I) all: 0.165 / Net I/σ(I): 20.99 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 2766 / CC1/2: 0.77 / CC star: 0.933 / Rpim(I) all: 0.35 / Rrim(I) all: 0.802 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EIC Resolution: 2.25→40.78 Å / SU ML: 0.3809 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.8137 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: 45.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→40.78 Å
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Refine LS restraints |
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LS refinement shell |
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