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Yorodumi- PDB-4x7b: Crystal Structure of lipase from Geobacillus stearothermophilus T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x7b | ||||||
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Title | Crystal Structure of lipase from Geobacillus stearothermophilus T6 methanol stable variant H86Y/A269T | ||||||
Components | Lipase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | triacylglycerol lipase / triglyceride lipase activity / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / triacylglycerol lipase Function and homology information | ||||||
Biological species | Geobacillus stearothermophilus T6 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Kanteev, M. / Dror, A. / Gihaz, S. / Fishman, A. | ||||||
Funding support | Israel, 1items
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Citation | Journal: Appl.Microbiol.Biotechnol. / Year: 2015 Title: Structural insights into methanol-stable variants of lipase T6 from Geobacillus stearothermophilus. Authors: Dror, A. / Kanteev, M. / Kagan, I. / Gihaz, S. / Shahar, A. / Fishman, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x7b.cif.gz | 90.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x7b.ent.gz | 70.5 KB | Display | PDB format |
PDBx/mmJSON format | 4x7b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/4x7b ftp://data.pdbj.org/pub/pdb/validation_reports/x7/4x7b | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 43900.969 Da / Num. of mol.: 1 / Fragment: UNP residues 34-418 / Mutation: H86Y, A269T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus T6 (bacteria) Plasmid: pET9a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93A71, triacylglycerol lipase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-CA / |
#4: 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: 2.33 Å3/Da / Density % sol: 47.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium citrate, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.56 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 7, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→60.778 Å / Num. all: 16204 / Num. obs: 16204 / % possible obs: 97.8 % / Redundancy: 3 % / Biso Wilson estimate: 22.99 Å2 / Rpim(I) all: 0.052 / Rrim(I) all: 0.092 / Rsym value: 0.075 / Net I/av σ(I): 8.267 / Net I/σ(I): 10 / Num. measured all: 48982 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30.272 Å / FOM work R set: 0.8175 / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.853 Å2 / ksol: 0.349 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.28 Å2 / Biso mean: 23.5 Å2 / Biso min: 9.97 Å2
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Refinement step | Cycle: final / Resolution: 2.4→30.272 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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