+Open data
-Basic information
Entry | Database: PDB / ID: 1rp1 | ||||||
---|---|---|---|---|---|---|---|
Title | DOG PANCREATIC LIPASE RELATED PROTEIN 1 | ||||||
Components | PANCREATIC LIPASE RELATED PROTEIN 1 | ||||||
Keywords | HYDROLASE / LIPID DEGRADATION / PANCREATIC LIPASE | ||||||
Function / homology | Function and homology information Digestion of dietary lipid / carboxylic ester hydrolase activity / lipid catabolic process / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Canis lupus familiaris (dog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Roussel, A. / Cambillau, C. | ||||||
Citation | Journal: Proteins / Year: 1998 Title: Reactivation of the totally inactive pancreatic lipase RP1 by structure-predicted point mutations. Authors: Roussel, A. / de Caro, J. / Bezzine, S. / Gastinel, L. / de Caro, A. / Carriere, F. / Leydier, S. / Verger, R. / Cambillau, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1rp1.cif.gz | 103.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1rp1.ent.gz | 79.9 KB | Display | PDB format |
PDBx/mmJSON format | 1rp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/1rp1 ftp://data.pdbj.org/pub/pdb/validation_reports/rp/1rp1 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1thgS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 49676.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / Organ: PANCREAS / Secretion: PANCREATIC JUICE / Species: Canis lupus / Strain: familiaris / References: UniProt: P06857, triacylglycerol lipase |
---|---|
#2: Sugar | ChemComp-NAG / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 4.2 Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 8000 WITH 25MM POTASSIUM PHOSPHATE BUFFER AT PH 4.2. | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusionDetails: drop was diluted with an equal volume of the reservoir solution | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: SPHERICAL GRATING MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→9 Å / Num. obs: 30017 / % possible obs: 97.8 % / Observed criterion σ(I): 1.5 / Redundancy: 3.4 % / Biso Wilson estimate: 33.17 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 3 / Rsym value: 0.368 / % possible all: 94.6 |
Reflection shell | *PLUS % possible obs: 94.6 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1THG Resolution: 2.1→9 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1300 / Data cutoff low absF: 70 / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→9 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.17 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.183 |