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Yorodumi- PDB-4ke8: Crystal structure of Monoglyceride lipase from Bacillus sp. H257 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ke8 | ||||||
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Title | Crystal structure of Monoglyceride lipase from Bacillus sp. H257 in complex with monopalmitoyl glycerol analogue | ||||||
Components | Thermostable monoacylglycerol lipase | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase / monoglyceride lipase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Rengachari, S. / Aschauer, P. / Gruber, K. / Dreveny, I. / Oberer, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Conformational plasticity and ligand binding of bacterial monoacylglycerol lipase. Authors: Rengachari, S. / Aschauer, P. / Schittmayer, M. / Mayer, N. / Gruber, K. / Breinbauer, R. / Birner-Gruenberger, R. / Dreveny, I. / Oberer, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ke8.cif.gz | 216.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ke8.ent.gz | 180 KB | Display | PDB format |
PDBx/mmJSON format | 4ke8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ke8_validation.pdf.gz | 1019.7 KB | Display | wwPDB validaton report |
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Full document | 4ke8_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4ke8_validation.xml.gz | 46.2 KB | Display | |
Data in CIF | 4ke8_validation.cif.gz | 67 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/4ke8 ftp://data.pdbj.org/pub/pdb/validation_reports/ke/4ke8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 29560.611 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: H-257 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P82597, acylglycerol lipase #2: Chemical | ChemComp-1QY / #3: 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: 2.23 Å3/Da / Density % sol: 44.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.2 Details: 0.1 M citric acid pH 5.2 and 18% PEG 3350, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 1, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→43.737 Å / Num. all: 88070 / Num. obs: 88070 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rsym value: 0.041 / Net I/σ(I): 17.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→43.737 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.18 / σ(F): 1.5 / Phase error: 26.86 / Stereochemistry target values: ML
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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 |
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Refinement step | Cycle: LAST / Resolution: 1.85→43.737 Å
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Refine LS restraints |
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LS refinement shell |
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