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Yorodumi- PDB-1pja: The crystal structure of palmitoyl protein thioesterase-2 reveals... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pja | ||||||
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Title | The crystal structure of palmitoyl protein thioesterase-2 reveals the basis for divergent substrate specificities of the two lysosomal thioesterases (PPT1 and PPT2) | ||||||
Components | Palmitoyl-protein thioesterase 2 precursor | ||||||
Keywords | HYDROLASE / glycoprotein / lysosome | ||||||
Function / homology | Function and homology information palmitoyl hydrolase activity / palmitoyl-(protein) hydrolase activity / thiolester hydrolase activity / fatty-acyl-CoA biosynthetic process / Fatty acyl-CoA biosynthesis / Hydrolases; Acting on ester bonds; Thioester hydrolases / lysosomal lumen / lysosome / intracellular membrane-bounded organelle / extracellular exosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Calero, G. / Gupta, P. / Nonato, M.C. / Tandel, S. / Biehl, E.R. / Hofmann, S.L. / Clardy, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pja.cif.gz | 63.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pja.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 1pja.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pja_validation.pdf.gz | 469.2 KB | Display | wwPDB validaton report |
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Full document | 1pja_full_validation.pdf.gz | 476.6 KB | Display | |
Data in XML | 1pja_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 1pja_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/1pja ftp://data.pdbj.org/pub/pdb/validation_reports/pj/1pja | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34342.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPT2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UMR5, palmitoyl[protein] hydrolase | ||
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#2: Sugar | ChemComp-NAG / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-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 | ||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.943 Å |
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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: 0.943 Å / Relative weight: 1 |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→40 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.7→40 Å
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.225 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS
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