+Open data
-Basic information
Entry | Database: PDB / ID: 7ozm | |||||||||
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Title | Crystal Structure of mtbMGL K74A (Closed Cap Conformation) | |||||||||
Components | Monoacylglycerol lipase | |||||||||
Keywords | HYDROLASE / Mycobacterium tuberculosis / monoacylglycerol lipase | |||||||||
Function / homology | Function and homology information glycerolipid catabolic process / acylglycerol lipase / monoacylglycerol lipase activity / lipase activity / peptidoglycan-based cell wall / symbiont-mediated activation of host apoptosis / extracellular region / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 | 7ozm.cif.gz | 84.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ozm.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ozm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ozm_validation.pdf.gz | 441.6 KB | Display | wwPDB validaton report |
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Full document | 7ozm_full_validation.pdf.gz | 443.3 KB | Display | |
Data in XML | 7ozm_validation.xml.gz | 13 KB | Display | |
Data in CIF | 7ozm_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/7ozm ftp://data.pdbj.org/pub/pdb/validation_reports/oz/7ozm | HTTPS FTP |
-Related structure data
Related structure data | 7p0yC 6eicS 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
#1: Protein | Mass: 33618.047 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-IPA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 15 % 2-propanol, 24 % PEG 3350, 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, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0723 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→39.77 Å / Num. obs: 16663 / % possible obs: 97.22 % / Redundancy: 3.3 % / Biso Wilson estimate: 29.19 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.086 / Rrim(I) all: 0.167 / Net I/σ(I): 7.27 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 1.43 / Num. unique obs: 1655 / CC1/2: 0.578 / CC star: 0.856 / Rpim(I) all: 0.462 / Rrim(I) all: 0.889 / % possible all: 97.93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6eic Resolution: 2.15→39.77 Å / SU ML: 0.3201 / Cross valid method: FREE R-VALUE / σ(F): 0.83 / Phase error: 26.7245 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: 29.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→39.77 Å
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Refine LS restraints |
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LS refinement shell |
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