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Yorodumi- PDB-1fx9: CARBOXYLIC ESTER HYDROLASE COMPLEX (DIMERIC PLA2 + MJ33 INHIBITOR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fx9 | ||||||
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Title | CARBOXYLIC ESTER HYDROLASE COMPLEX (DIMERIC PLA2 + MJ33 INHIBITOR + SULPHATE IONS) | ||||||
Components | PHOSPHOLIPASE A2, MAJOR ISOENZYME | ||||||
Keywords | HYDROLASE / ENZYME / CARBOXYLIC ESTER HYDROLASE / DIMER / SULPHATE BINDING / INHIBITOR 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: 2 Å | ||||||
Authors | Pan, Y.H. / Epstein, T.M. / Jain, M.K. / Bahnson, B.J. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Five coplanar anion binding sites on one face of phospholipase A2: relationship to interface binding. Authors: Pan, Y.H. / Epstein, T.M. / 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 | 1fx9.cif.gz | 66.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fx9.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 1fx9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/1fx9 ftp://data.pdbj.org/pub/pdb/validation_reports/fx/1fx9 | HTTPS FTP |
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-Related structure data
Related structure data | 1fxfC 4p2pS C: citing same article (ref.) 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: 14009.714 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli (E. coli) / References: UniProt: P00592, phospholipase A2 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MJI / | #5: 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 Å3/Da / Density % sol: 54.95 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 4.6 Details: 25% PEG3500, 0.2 M SODIUM SULPHATE, 0.1 M SODIUM ACETATE BUFFER, PH 4.6, EVAPORATION, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
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 RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 22, 2000 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30.44 Å / Num. all: 122013 / Num. obs: 19393 / % possible obs: 96.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1996 / % possible all: 98.3 |
Reflection | *PLUS Num. measured all: 122013 / Rmerge(I) obs: 0.068 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 4P2P Resolution: 2→8 Å / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER Details: MEROHEDRAL TWINNING REFINEMENT USING SHELXL-97. XPLOR-3.1, SHELXL-97 were also used during refinement.
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.171 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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