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- PDB-3fvi: Crystal Structure of Complex of Phospholipase A2 with Octyl Sulfates -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fvi | ||||||
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Title | Crystal Structure of Complex of Phospholipase A2 with Octyl Sulfates | ||||||
![]() | Phospholipase A2, major isoenzyme | ||||||
![]() | HYDROLASE / Phospholipase A2 / Pla2-1B / octyl sulfate binding / protein detergent aggregates / Lipid degradation / Lipoprotein / Metal-binding / Palmitate / Pyrrolidone carboxylic acid / Secreted | ||||||
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. | ||||||
![]() | ![]() Title: Structure of a premicellar complex of alkyl sulfates with the interfacial binding surfaces of four subunits of 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 | ![]() | 113.1 KB | Display | ![]() |
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PDB format | ![]() | 88.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3fvjC ![]() 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 14009.714 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 84 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/OSF.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/OSF.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | ChemComp-OSF / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.88 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M sodium acetate, 8% w/v PEG 8000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 10, 2003 / Details: mirrors |
Radiation | Monochromator: Ni Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→33.54 Å / Num. all: 19134 / Num. obs: 18967 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.119 / Rsym value: 0.093 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 8 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1823 / Rsym value: 0.415 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1FXF Resolution: 2.7→33.54 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 178032.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 11.4417 Å2 / ksol: 0.326809 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.9 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→33.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
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Xplor file |
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