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Yorodumi- PDB-3d2b: Structure of 2D9, a thermostable mutant of Bacillus subtilis lipa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d2b | ||||||
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Title | Structure of 2D9, a thermostable mutant of Bacillus subtilis lipase obtained through directed evolution | ||||||
Components | Lipase | ||||||
Keywords | HYDROLASE / lipase / alpha/beta hydrolase / stability / directed evolution / Lipid degradation / Secreted | ||||||
Function / homology | Function and homology information lipase activity / triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å | ||||||
Authors | Sankaranarayanan, R. / Kamal, M.Z. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Thermostable Bacillus subtilis lipases: in vitro evolution and structural insight Authors: Ahmad, S. / Kamal, M.Z. / Sankaranarayanan, R. / Rao, N.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d2b.cif.gz | 83.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d2b.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 3d2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/3d2b ftp://data.pdbj.org/pub/pdb/validation_reports/d2/3d2b | 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: 19466.889 Da / Num. of mol.: 2 / Mutation: F17S, N89Y, L114P, A132D, I157M, N166Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: lipA, lip, BSU02700 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37957, triacylglycerol lipase #2: 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: 3.33 Å3/Da / Density % sol: 63.09 % / Mosaicity: 0.593 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 100mM Ethanolamine buffe, 10mM Sodium sulfate, pH 9.5, vapour diffusion, sitting drop, temperature 277K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: osmic mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→25 Å / Num. obs: 36223 / % possible obs: 94.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.066 / Χ2: 0.561 / Net I/σ(I): 10.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.95→25 Å / FOM work R set: 0.885 / σ(F): 0
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Solvent computation | Bsol: 41.541 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.955 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→25 Å
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Refine LS restraints |
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Xplor file |
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