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- PDB-4x7b: Crystal Structure of lipase from Geobacillus stearothermophilus T... -
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Open data
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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 | ||||||
![]() | Lipase | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kanteev, M. / Dror, A. / Gihaz, S. / Fishman, A. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.8 KB | Display | ![]() |
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PDB format | ![]() | 69.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419.9 KB | Display | ![]() |
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Full document | ![]() | 421.8 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 23.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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. |
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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.) ![]() ![]() Plasmid: pET9a / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | Wavelength: 1.56 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: _
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]()
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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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