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Open data
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Basic information
Entry | Database: PDB / ID: 4x92 | ||||||
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Title | Crystal structure of Lysosomal Phospholipase A2-S165A | ||||||
![]() | Group XV phospholipase A2 | ||||||
![]() | TRANSFERASE / hydrolase / phospholipase / esterase / acyltransferase | ||||||
Function / homology | ![]() acylglycerol O-acyltransferase activity / phosphatidylethanolamine catabolic process / Hydrolysis of LPC / phosphatidylserine metabolic process / phosphatidyl phospholipase B activity / lysophospholipase / glycerophospholipid metabolic process / phospholipase A1 / O-acyltransferase activity / phosphatidylserine 1-acylhydrolase activity ...acylglycerol O-acyltransferase activity / phosphatidylethanolamine catabolic process / Hydrolysis of LPC / phosphatidylserine metabolic process / phosphatidyl phospholipase B activity / lysophospholipase / glycerophospholipid metabolic process / phospholipase A1 / O-acyltransferase activity / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / calcium-independent phospholipase A2 activity / diacylglycerol biosynthetic process / phosphatidylglycerol metabolic process / ceramide metabolic process / phosphatidylcholine catabolic process / fatty acid catabolic process / phosphatidylcholine metabolic process / lysophospholipase activity / phospholipase A2 / phospholipid metabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / phospholipid binding / lysosome / intracellular membrane-bounded organelle / extracellular space / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Glukhova, A. / Tesmer, J.J.G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and function of lysosomal phospholipase A2 and lecithin:cholesterol acyltransferase. Authors: Glukhova, A. / Hinkovska-Galcheva, V. / Kelly, R. / Abe, A. / Shayman, J.A. / Tesmer, J.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 | ![]() | 166.2 KB | Display | ![]() |
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PDB format | ![]() | 133.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.2 KB | Display | ![]() |
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Full document | ![]() | 449.9 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4x90SC ![]() 4x91C ![]() 4x93C ![]() 4x94C ![]() 4x95C ![]() 4x96C ![]() 4x97C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 43105.027 Da / Num. of mol.: 1 / Fragment: UNP residues 34-412 / Mutation: S165A Source method: isolated from a genetically manipulated source Details: S165A mutant of human Lysosomal Phospholipase A2 / Source: (gene. exp.) ![]() ![]() References: UniProt: Q8NCC3, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups | ||
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#2: Sugar | ChemComp-NAG / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.13 Å3/Da / Density % sol: 70.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM Na cacodylate pH 6.5, 10% PEG 8000, 200 mM Mg(CH3COO) in the presence of DOPC liposomes |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 14, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→30 Å / Num. obs: 14922 / % possible obs: 98.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.098 / Rrim(I) all: 0.23 / Χ2: 1.115 / Net I/av σ(I): 8.938 / Net I/σ(I): 3.9 / Num. measured all: 83833 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4X90 Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / SU B: 26.723 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.78 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.48 Å2 / Biso mean: 43.389 Å2 / Biso min: 3.99 Å2
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Refinement step | Cycle: final / Resolution: 3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.002→3.079 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -26.8048 Å / Origin y: 60.1309 Å / Origin z: 37.3837 Å
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