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Yorodumi- PDB-6isq: structure of Lipase mutant with oxided Cys-His-Asp catalytic triad -
+Open data
-Basic information
Entry | Database: PDB / ID: 6isq | ||||||
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Title | structure of Lipase mutant with oxided Cys-His-Asp catalytic triad | ||||||
Components | Lipase B | ||||||
Keywords | HYDROLASE / Calb | ||||||
Function / homology | Function and homology information triacylglycerol lipase / triglyceride lipase activity / lipid catabolic process Similarity search - Function | ||||||
Biological species | Pseudozyma antarctica (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Cen, Y.X. / Zhou, J.H. / Wu, Q. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Artificial cysteine-lipases with high activity and altered catalytic mechanism created by laboratory evolution. Authors: Cen, Y. / Singh, W. / Arkin, M. / Moody, T.S. / Huang, M. / Zhou, J. / Wu, Q. / Reetz, M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6isq.cif.gz | 255.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6isq.ent.gz | 205.9 KB | Display | PDB format |
PDBx/mmJSON format | 6isq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/6isq ftp://data.pdbj.org/pub/pdb/validation_reports/is/6isq | HTTPS FTP |
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-Related structure data
Related structure data | 6ispC 6isrC 1tcaS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 33473.734 Da / Num. of mol.: 2 / Mutation: T57A, A89T, W104V, S105CSD, V149G, A281Y, A282Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudozyma antarctica (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41365, triacylglycerol lipase |
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-Non-polymers , 5 types, 309 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.9 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium acetate, pH 6.0 25% PEG4000 8% isopropanol 0.5% N,N-dimethyldodecylamine oxide(DDAO) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. obs: 51204 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.86→1.89 Å / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 2 / Num. unique obs: 2499 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TCA Resolution: 1.86→37.038 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.75
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→37.038 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: 55.3872 Å / Origin y: 0.1516 Å / Origin z: 52.6137 Å
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Refinement TLS group | Selection details: all |