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Yorodumi- PDB-1f6w: STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN BILE SALT ACTIVATED LIPASE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f6w | ||||||
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Title | STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN BILE SALT ACTIVATED LIPASE | ||||||
Components | BILE SALT ACTIVATED LIPASE | ||||||
Keywords | HYDROLASE / bile salt activated lipase / esterase / catalytic domain | ||||||
Function / homology | Function and homology information retinyl-palmitate esterase activity / Digestion of dietary lipid / acetylesterase / ceramide catabolic process / sterol esterase / sterol ester 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 ester esterase activity / pancreatic juice secretion / acetylesterase activity / intestinal cholesterol absorption / triacylglycerol lipase / triacylglycerol 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: 2.3 Å | ||||||
Authors | Terzyan, S. / Zhang, X. | ||||||
Citation | Journal: Protein Sci. / Year: 2000 Title: Crystal structure of the catalytic domain of human bile salt activated lipase. Authors: Terzyan, S. / Wang, C.S. / Downs, D. / Hunter, B. / Zhang, X.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f6w.cif.gz | 118.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f6w.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 1f6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/1f6w ftp://data.pdbj.org/pub/pdb/validation_reports/f6/1f6w | HTTPS FTP |
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-Related structure data
Related structure data | 1aknS S: Starting model for refinement |
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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: 58826.695 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: A298D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: PANCREAS / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: P19835, triacylglycerol lipase |
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#2: 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: 2.6 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 6.5 Details: PEG 6000, NaCl, N-(2-acetamido) iminodiacetic acid, pH 6.5, EVAPORATION, temperature 293.K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978 |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Oct 26, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 27725 / Num. obs: 25287 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 45.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2378 / % possible all: 87.8 |
Reflection shell | *PLUS % possible obs: 87.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AKN Resolution: 2.3→24.19 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 157890557.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Bulk Solvent Model Used
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.2893 Å2 / ksol: 0.28 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→24.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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