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Yorodumi- PDB-6fz7: Crystal Structure of lipase from Geobacillus stearothermophilus T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fz7 | ||||||
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Title | Crystal Structure of lipase from Geobacillus stearothermophilus T6 methanol stable variant L184F | ||||||
Components | Lipase | ||||||
Keywords | HYDROLASE / lipase / methanol / organic solvent | ||||||
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: 1.736 Å | ||||||
Authors | Gihaz, S. / Kanteev, M. / Pazy, Y. / Fishman, A. | ||||||
Citation | Journal: Appl.Environ.Microbiol. / Year: 2018 Title: Filling the Void: Introducing Aromatic Interactions into Solvent Tunnels To Enhance Lipase Stability in Methanol. Authors: Gihaz, S. / Kanteev, M. / 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 | 6fz7.cif.gz | 180.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fz7.ent.gz | 141.6 KB | Display | PDB format |
PDBx/mmJSON format | 6fz7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fz7_validation.pdf.gz | 417.6 KB | Display | wwPDB validaton report |
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Full document | 6fz7_full_validation.pdf.gz | 419.9 KB | Display | |
Data in XML | 6fz7_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 6fz7_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/6fz7 ftp://data.pdbj.org/pub/pdb/validation_reports/fz/6fz7 | HTTPS FTP |
-Related structure data
Related structure data | 6fz1C 6fz8C 6fz9C 6fzaC 6fzcC 6fzdC 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: 43967.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) 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: 47.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium citrate, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07227 Å / Relative weight: 1 |
Reflection | Resolution: 1.736→57.255 Å / Num. obs: 43045 / % possible obs: 99.4 % / Redundancy: 5.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.09 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.736→1.736 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4X6U Resolution: 1.736→57.255 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.736→57.255 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -10.5673 Å / Origin y: 11.0237 Å / Origin z: -18.5546 Å
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Refinement TLS group | Selection details: all |