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Yorodumi- PDB-1t2n: Structure of a thermostable triple mutant of Bacillus subtilis li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t2n | ||||||
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Title | Structure of a thermostable triple mutant of Bacillus subtilis lipase obtained through directed evolution | ||||||
Components | Lipase | ||||||
Keywords | HYDROLASE / ALPHA/BETA HYDROLASE | ||||||
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 / Resolution: 1.8 Å | ||||||
Authors | Rajakumara, E. / Sankaranarayanan, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Structural basis of selection and thermostability of laboratory evolved Bacillus subtilis lipase. Authors: Acharya, P. / Rajakumara, E. / Sankaranarayanan, R. / Rao, N.M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Crystallization and preliminary X-ray crystallographic investigations on several thermostable forms of a Bacillus subtilis lipase. Authors: Rajakumara, E. / Acharya, P. / Ahmad, S. / Shanmugam, V.M. / Rao, N.M. / Sankaranarayanan, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t2n.cif.gz | 52.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t2n.ent.gz | 36.2 KB | Display | PDB format |
PDBx/mmJSON format | 1t2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t2n_validation.pdf.gz | 406.4 KB | Display | wwPDB validaton report |
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Full document | 1t2n_full_validation.pdf.gz | 407.1 KB | Display | |
Data in XML | 1t2n_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 1t2n_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/1t2n ftp://data.pdbj.org/pub/pdb/validation_reports/t2/1t2n | HTTPS FTP |
-Related structure data
Related structure data | 1t4mC 1i6wS 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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Unit cell |
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Details | The monomer found in the asu is the biologically functional unit. |
-Components
#1: Protein | Mass: 19459.875 Da / Num. of mol.: 1 / Mutation: L114P, A132D, N166Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: LIPA, LIP, BSU02700 / Plasmid: pET-21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37957, triacylglycerol lipase |
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#2: Chemical | ChemComp-K / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: PEG 3350, ethanolamine, n-octyl-beta-D-glucoside, sodium sulfate, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 2003 / Details: Osmic |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. all: 20416 / Num. obs: 20289 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 20.3 Å2 / Rsym value: 0.026 / Net I/σ(I): 32 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2 % / Mean I/σ(I) obs: 4 / Num. unique all: 1918 / Rsym value: 0.161 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I6W Resolution: 1.8→24.14 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1521273.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The ion present in the coordinates was named potassium based on the B-factor during refinement.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 111.926 Å2 / ksol: 0.520093 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→24.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
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Xplor file |
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