+Open data
-Basic information
Entry | Database: PDB / ID: 1bu8 | ||||||
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Title | RAT PANCREATIC LIPASE RELATED PROTEIN 2 | ||||||
Components | PROTEIN (PANCREATIC LIPASE RELATED PROTEIN 2) | ||||||
Keywords | HYDROLASE / LIPID DEGRADATION / PANCREATIC LIPASE | ||||||
Function / homology | Function and homology information intestinal lipid catabolic process / Digestion of dietary lipid / galactolipid catabolic process / galactolipase activity / : / galactolipase / triglyceride catabolic process / phospholipase activity / monoacylglycerol lipase activity / zymogen granule membrane ...intestinal lipid catabolic process / Digestion of dietary lipid / galactolipid catabolic process / galactolipase activity / : / galactolipase / triglyceride catabolic process / phospholipase activity / monoacylglycerol lipase activity / zymogen granule membrane / phospholipid catabolic process / lipase activity / phosphatidylcholine catabolic process / triacylglycerol lipase / triacylglycerol lipase activity / response to food / response to lipid / phospholipid metabolic process / cellular defense response / response to glucocorticoid / post-embryonic development / response to bacterium / response to peptide hormone / neuron projection / calcium ion binding / extracellular space Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Roussel, A. / Cambillau, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Structure and activity of rat pancreatic lipase-related protein 2. Authors: Roussel, A. / Yang, Y. / Ferrato, F. / Verger, R. / Cambillau, C. / Lowe, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bu8.cif.gz | 108.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bu8.ent.gz | 80.8 KB | Display | PDB format |
PDBx/mmJSON format | 1bu8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bu8_validation.pdf.gz | 441.5 KB | Display | wwPDB validaton report |
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Full document | 1bu8_full_validation.pdf.gz | 447.2 KB | Display | |
Data in XML | 1bu8_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 1bu8_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/1bu8 ftp://data.pdbj.org/pub/pdb/validation_reports/bu/1bu8 | HTTPS FTP |
-Related structure data
Related structure data | 1thgS 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: 50920.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: PANCREAS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P54318, triacylglycerol lipase |
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#2: Sugar | ChemComp-NAG / |
#3: 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: 2.66 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.4 Details: PROTEIN WAS CRYSTALLIZED FROM 8% PEG 8000 WITH 0.1 M TRIS/HCL PH 8.4 | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 / Method: vapor diffusion, hanging drop / Details: used to seeding | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1997 / Details: MIRRORS |
Radiation | Monochromator: LURE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→10 Å / Num. obs: 47899 / % possible obs: 97.5 % / Observed criterion σ(I): 1.5 / Redundancy: 2.4 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.42 / % possible all: 81.9 |
Reflection shell | *PLUS % possible obs: 81.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1THG Resolution: 1.8→10 Å / Data cutoff high absF: 750 / Data cutoff low absF: 50 / σ(F): 2
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Displacement parameters | Biso mean: 20.78 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.83 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS % reflection Rfree: 5 % |