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- PDB-2b01: Crystal Structure of Porcine Pancreatic Phospholipase A2 in Compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2b01 | ||||||
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Title | Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Taurochenodeoxycholate | ||||||
![]() | Phospholipase A2, major isoenzyme | ||||||
![]() | HYDROLASE / Bile Salt / Taurochenodeoxycholate / Carboxylic ester hydrolase / PLA2 / Pancreatic Enzyme | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pan, Y.H. / Bahnson, B.J. / Jain, M.K. | ||||||
![]() | ![]() Title: Structural basis for bile salt inhibition of pancreatic phospholipase A2. Authors: Pan, Y.H. / Bahnson, B.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44 KB | Display | ![]() |
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PDB format | ![]() | 28.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 721 KB | Display | ![]() |
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Full document | ![]() | 726.1 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 12.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2azyC ![]() 2azzC ![]() 2b00C ![]() 2b03C ![]() 2b04C ![]() 1fxfS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 14009.714 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-TUD / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M Calcium Chloride, 28% PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 2, 2004 / Details: Mirrors |
Radiation | Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→100 Å / Num. obs: 9562 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.05 / Net I/σ(I): 27 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.9 / Num. unique all: 946 / Rsym value: 0.317 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1FXF Resolution: 2.2→27.08 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 336324.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→27.08 Å
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Refine LS restraints |
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Xplor file |
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