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Yorodumi- PDB-6s3g: Crystal Structure of lipase from Geobacillus stearothermophilus T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s3g | ||||||
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Title | Crystal Structure of lipase from Geobacillus stearothermophilus T6 variant A187C/F291C | ||||||
Components | Lipase | ||||||
Keywords | HYDROLASE / lipase / methanol / organic solvent / disulfide bond | ||||||
Function / homology | triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / Alpha/Beta hydrolase fold / extracellular region / metal ion binding / triacylglycerol lipase Function and homology information | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Gihaz, S. / Bash, Y. / Rush, I. / Shahar, A. / Pazy, Y. / Fishman, A. | ||||||
Citation | Journal: Chemcatchem / Year: 2019 Title: Bridges to Stability: Engineering Disulfide Bonds Towards Enhanced Lipase Biodiesel Synthesis Authors: Gihaz, S. / Bash, Y. / Rush, I. / Shahar, A. / Pazy, Y. / Fishman, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s3g.cif.gz | 97.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s3g.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 6s3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/6s3g ftp://data.pdbj.org/pub/pdb/validation_reports/s3/6s3g | HTTPS FTP |
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-Related structure data
Related structure data | 6s3jC 6s3vC 4x6uS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 43921.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Plasmid: pET9a / Production host: Escherichia coli (E. coli) / Variant (production host): SHuffle / References: UniProt: Q93A71, triacylglycerol lipase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2M sodium citrate, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.48 Å / Num. obs: 32881 / % possible obs: 100 % / Redundancy: 4.1 % / Biso Wilson estimate: 24.77 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.08 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 4711 / CC1/2: 0.777 / Rrim(I) all: 0.769 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4X6U Resolution: 1.9→44.48 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 27.62 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→44.48 Å
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