[English] 日本語
![](img/lk-miru.gif)
- PDB-1pja: The crystal structure of palmitoyl protein thioesterase-2 reveals... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1pja | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of palmitoyl protein thioesterase-2 reveals the basis for divergent substrate specificities of the two lysosomal thioesterases (PPT1 and PPT2) | ||||||
![]() | Palmitoyl-protein thioesterase 2 precursor | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() palmitoyl hydrolase activity / palmitoyl-(protein) hydrolase activity / fatty-acyl-CoA biosynthetic process / thiolester hydrolase activity / Fatty acyl-CoA biosynthesis / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Calero, G. / Gupta, P. / Nonato, M.C. / Tandel, S. / Biehl, E.R. / Hofmann, S.L. / Clardy, J. | ||||||
![]() | ![]() Title: The crystal structure of palmitoyl protein thioesterase-2 (PPT2) reveals the basis for divergent substrate specificities of the two lysosomal thioesterases, PPT1 and PPT2. Authors: Calero, G. / Gupta, P. / Nonato, M.C. / Tandel, S. / Biehl, E.R. / Hofmann, S.L. / Clardy, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 63.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 50.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 34342.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||
---|---|---|---|
#2: Sugar | ChemComp-NAG / ![]() | ||
#3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1.8-2.2M ammonium sulfate, 8% methyl-pentane-diol, 100 mM MES , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop / PH range low: 6.5 / PH range high: 5.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
---|---|
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→40 Å / Num. all: 34721 / Num. obs: 34721 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rsym value: 0.046 / Net I/σ(I): 15.7 |
Reflection shell | Highest resolution: 2.7 Å / Mean I/σ(I) obs: 2.5 |
Reflection | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.046 |
-
Processing
Software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]()
| ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→40 Å
| ||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree![]() ![]() | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS
|