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Yorodumi- PDB-1l8s: CARBOXYLIC ESTER HYDROLASE COMPLEX (DIMERIC PLA2 + LPC-ether + AC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l8s | ||||||
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Title | CARBOXYLIC ESTER HYDROLASE COMPLEX (DIMERIC PLA2 + LPC-ether + ACETATE + PHOSPHATE IONS) | ||||||
Components | PHOSPHOLIPASE A2, MAJOR ISOENZYME | ||||||
Keywords | HYDROLASE / ENZYME / CARBOXYLIC ESTER HYDROLASE / DIMER / PAF HYDROLYSIS PRODUCTS BINDING / PHOSPHATE BINDING | ||||||
Function / homology | Function and homology information positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / phospholipase A2 activity / leukotriene biosynthetic process / neutrophil mediated immunity / calcium-dependent phospholipase A2 activity / phospholipase A2 / bile acid binding ...positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / phospholipase A2 activity / leukotriene biosynthetic process / neutrophil mediated immunity / calcium-dependent phospholipase A2 activity / phospholipase A2 / bile acid binding / positive regulation of calcium ion transport into cytosol / phospholipid metabolic process / lipid catabolic process / neutrophil chemotaxis / positive regulation of interleukin-8 production / positive regulation of MAP kinase activity / phospholipid binding / fatty acid biosynthetic process / cellular response to insulin stimulus / positive regulation of immune response / positive regulation of fibroblast proliferation / positive regulation of NF-kappaB transcription factor activity / intracellular signal transduction / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / cell surface / positive regulation of transcription by RNA polymerase II / extracellular region Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Pan, Y.H. / Bahnson, B.J. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Crystal structure of phospholipase A2 Complex with the Hydrolysis Products of Platelet Activating Factor: Equilibrium Binding of Fatty Acid and Lysophospholipid-ether at the Active Site may be Mutually Exclusive Authors: Pan, Y.H. / Yu, B.-Z. / Berg, O.G. / Jain, M.K. / Bahnson, B.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l8s.cif.gz | 67.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l8s.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 1l8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/1l8s ftp://data.pdbj.org/pub/pdb/validation_reports/l8/1l8s | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 14009.714 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Organ: PANCREAS / Production host: Escherichia coli (E. coli) / References: UniProt: P00592, phospholipase A2 |
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-Non-polymers , 6 types, 322 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-ACT / | #6: Chemical | ChemComp-LPE / | #7: 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: 2.06 Å3/Da / Density % sol: 40.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, CALCIUM CHLORIDE, PAF, SODIUM ACETATE, SODIUM PHOSPHATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 25K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 17, 2000 / Details: MIRRORS |
Radiation | Monochromator: OS MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→100 Å / Num. all: 43474 / Num. obs: 43050 / % possible obs: 26 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 3 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.7 / Num. unique all: 4130 / % possible all: 95.9 |
Reflection | *PLUS Lowest resolution: 100 Å / % possible obs: 99 % / Num. measured all: 266326 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 95.9 % / Rmerge(I) obs: 0.36 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→8 Å / Num. parameters: 9231 / Num. restraintsaints: 8183 / Isotropic thermal model: isotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER Details: IN THE LPC-ETHER LIGAND MODEL, ONLY ATOMS C20 TO C28 OF THE SN-1 ACYL CHAIN WERE ORDERED AS TWO ALTERNATE CONFORMATIONS. FOR ILLUSTRATION PURPOSE ONLY, ONE COPY OF A COMPLETE LPC-ETHER MODEL ...Details: IN THE LPC-ETHER LIGAND MODEL, ONLY ATOMS C20 TO C28 OF THE SN-1 ACYL CHAIN WERE ORDERED AS TWO ALTERNATE CONFORMATIONS. FOR ILLUSTRATION PURPOSE ONLY, ONE COPY OF A COMPLETE LPC-ETHER MODEL IS INCLUDED IN THE PDB WHERE OCCUPANCIES AS WELL AS TEMPERATURE FACTORS OF THE DISORDERED ATOMS WERE ASSIGN TO ZERO DURING THE FINAL ROUND OF REFINEMENT.
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2307 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→8 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.249 / Rfactor Rwork: 0.184 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_angle_d / Dev ideal: 0.028 |