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Yorodumi- PDB-1r50: Bacillus subtilis lipase A with covalently bound Sc-IPG-phosphona... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r50 | ||||||
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Title | Bacillus subtilis lipase A with covalently bound Sc-IPG-phosphonate-inhibitor | ||||||
Components | Lipase | ||||||
Keywords | HYDROLASE / lipase / alpha/beta hydrolase / phosphonate inhibitor | ||||||
Function / homology | Function and homology information lipase activity / triacylglycerol lipase / triglyceride lipase activity / lipid catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Droege, M.J. / Van Pouderoyen, G. / Vrenken, T.E. / Rueggeberg, C.J. / Reetz, M.T. / Dijkstra, B.W. / Quax, W.J. | ||||||
Citation | Journal: Chembiochem / Year: 2005 Title: Directed Evolution of Bacillus subtilis Lipase A by Use of Enantiomeric Phosphonate Inhibitors: Crystal Structures and Phage Display Selection Authors: Droege, M.J. / Boersma, Y.L. / van Pouderoyen, G. / Vrenken, T.E. / Rueggeberg, C.J. / Reetz, M.T. / Dijkstra, B.W. / Quax, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r50.cif.gz | 83.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r50.ent.gz | 63.4 KB | Display | PDB format |
PDBx/mmJSON format | 1r50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/1r50 ftp://data.pdbj.org/pub/pdb/validation_reports/r5/1r50 | HTTPS FTP |
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-Related 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: 19382.836 Da / Num. of mol.: 2 / Fragment: residues 1-181 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: lipA / Plasmid: PMA5LIP / Production host: Bacillus subtilis (bacteria) / Strain (production host): BCL1051 / References: UniProt: P37957, triacylglycerol lipase #2: Chemical | #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: 1.89 Å3/Da / Density % sol: 34.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10 Details: PEG 4000, ETHANOL AMINE, SODIUM SULPHATE, CADMIUM CHLORIDE, pH 10, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 10, 2001 / Details: MIRRORS |
Radiation | Monochromator: SI111 OR SI311 CRYSTALS, LN2 COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→100 Å / Num. all: 56823 / Num. obs: 48857 / % possible obs: 85.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 13.2 Å2 / Rsym value: 0.042 / Net I/σ(I): 27.3 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1001 / Rsym value: 0.305 / % possible all: 35.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Bacillus subtilis lipase A Resolution: 1.45→100 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 53 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.45→100 Å
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Refine LS restraints |
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