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Open data
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Basic information
Entry | Database: PDB / ID: 7zom | |||||||||
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Title | Crystal structure of N-terminal catalytic domain of human PLAAT3 | |||||||||
![]() | Phospholipase A and acyltransferase 3 | |||||||||
![]() | HYDROLASE / NlpC/P60 / catalytic domain / phospholipase A and acyltransferase / enterovirus host factor / membrane remodelling | |||||||||
Function / homology | ![]() membrane disassembly / ether lipid metabolic process / regulation of adipose tissue development / organelle disassembly / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity ...membrane disassembly / ether lipid metabolic process / regulation of adipose tissue development / organelle disassembly / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / peroxisome organization / N-acyltransferase activity / phospholipid biosynthetic process / phospholipase A2 activity / lens fiber cell differentiation / phospholipase A2 / peroxisomal membrane / triglyceride metabolic process / acyltransferase activity / localization / phospholipid metabolic process / lipid catabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / mitochondrial membrane / response to bacterium / peroxisome / nuclear envelope / lysosome / lysosomal membrane / lipid binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / mitochondrion / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | von Castelmur, E. / Perrakis, A. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Crystal structure of N-terminal catalytic domain of human PLAAT3 Authors: von Castelmur, E. / Perrakis, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.5 KB | Display | ![]() |
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PDB format | ![]() | 24.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.4 KB | Display | ![]() |
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Full document | ![]() | 434.4 KB | Display | |
Data in XML | ![]() | 7 KB | Display | |
Data in CIF | ![]() | 8.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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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: 14825.825 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P53816, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, phospholipase A1, phospholipase A2 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.61 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M Hepes-NaOH pH7.0-7.5, 45-70% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97632 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→42.84 Å / Num. obs: 21212 / % possible obs: 99.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.021 / Rrim(I) all: 0.039 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 999 / Rpim(I) all: 0.423 / Rrim(I) all: 0.779 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been used if present in the input file
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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: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.16 Å2
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Refinement step | Cycle: LAST / Resolution: 1.601→42.84 Å
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Refine LS restraints |
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LS refinement shell |
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