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Yorodumi- PDB-6h0t: Crystal structure of native recombinant human bile salt activated... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h0t | |||||||||
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Title | Crystal structure of native recombinant human bile salt activated lipase | |||||||||
Components | Bile salt-activated lipase | |||||||||
Keywords | HYDROLASE / Lipase / alpha-beta hydrolase. | |||||||||
Function / homology | Function and homology information retinyl-palmitate esterase activity / Digestion of dietary lipid / acetylesterase / ceramide catabolic process / sterol esterase / sterol esterase activity / pancreatic juice secretion / acetylesterase activity / intestinal cholesterol absorption / triacylglycerol lipase ...retinyl-palmitate esterase activity / Digestion of dietary lipid / acetylesterase / ceramide catabolic process / sterol esterase / sterol esterase activity / pancreatic juice secretion / acetylesterase activity / intestinal cholesterol absorption / triacylglycerol lipase / triglyceride lipase activity / catalytic activity / lipid metabolic process / heparin binding / hydrolase activity / extracellular space / extracellular exosome / extracellular region / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Touvrey, C. / Brazzolotto, X. / Nachon, F. | |||||||||
Funding support | France, 2items
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Citation | Journal: Toxicology / Year: 2019 Title: X-ray structures of human bile-salt activated lipase conjugated to nerve agents surrogates. Authors: Touvrey, C. / Courageux, C. / Guillon, V. / Terreux, R. / Nachon, F. / Brazzolotto, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h0t.cif.gz | 145.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h0t.ent.gz | 89.9 KB | Display | PDB format |
PDBx/mmJSON format | 6h0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/6h0t ftp://data.pdbj.org/pub/pdb/validation_reports/h0/6h0t | HTTPS FTP |
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-Related structure data
Related structure data | 6h0vC 6h18C 6h19C 6h1aC 1f6wS 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: 60742.715 Da / Num. of mol.: 1 / Mutation: N186D, A298D, 534STOP Source method: isolated from a genetically manipulated source Details: Crystals with uncleaved tagged enzyme / Source: (gene. exp.) Homo sapiens (human) / Gene: CEL, BAL / Production host: Cricetulus griseus (Chinese hamster) References: UniProt: P19835, sterol esterase, triacylglycerol lipase | ||||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-GOL / | #5: 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: 2.74 Å3/Da / Density % sol: 55.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, cacodylate, zinc acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2015 |
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→39.93 Å / Num. obs: 49920 / % possible obs: 99.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 35.21 Å2 / Rmerge(I) obs: 0.08457 / Rpim(I) all: 0.04367 / Rrim(I) all: 0.09572 / Net I/σ(I): 8.07 |
Reflection shell | Resolution: 1.9→1.968 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.231 / Num. unique obs: 4887 / Rpim(I) all: 0.6223 / Rrim(I) all: 1.386 / % possible all: 99.17 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1f6w Resolution: 1.9→39.93 Å / SU ML: 0.254 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.5616
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→39.93 Å
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Refine LS restraints |
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LS refinement shell |
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