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Yorodumi- PDB-3edy: Crystal Structure of the Precursor Form of Human Tripeptidyl-Pept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3edy | ||||||
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Title | Crystal Structure of the Precursor Form of Human Tripeptidyl-Peptidase 1 | ||||||
Components | Tripeptidyl-peptidase 1 | ||||||
Keywords | HYDROLASE / protease / TPP1 / sedolisin / Batten disease / LINCL / zymogen / prodomain / exopeptidase / endopeptidase / S53 family / cln2 / catalytic triad / oxyanion hole / Disease mutation / Epilepsy / Glycoprotein / Lysosome / Neuronal ceroid lipofuscinosis / Serine protease | ||||||
Function / homology | Function and homology information tripeptidyl-peptidase I / sulfatide binding / lysophosphatidic acid binding / lysosomal protein catabolic process / tripeptidyl-peptidase activity / XBP1(S) activates chaperone genes / protein localization to chromosome, telomeric region / lysosome organization / peptide catabolic process / neuromuscular process controlling balance ...tripeptidyl-peptidase I / sulfatide binding / lysophosphatidic acid binding / lysosomal protein catabolic process / tripeptidyl-peptidase activity / XBP1(S) activates chaperone genes / protein localization to chromosome, telomeric region / lysosome organization / peptide catabolic process / neuromuscular process controlling balance / bone resorption / epithelial cell differentiation / serine-type peptidase activity / lysosomal lumen / central nervous system development / peptide binding / protein catabolic process / lipid metabolic process / recycling endosome / melanosome / nervous system development / peptidase activity / endopeptidase activity / lysosome / membrane raft / serine-type endopeptidase activity / Golgi apparatus / proteolysis / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å | ||||||
Authors | Guhaniyogi, J. / Sohar, I. / Das, K. / Lobel, P. / Stock, A.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Crystal Structure and Autoactivation Pathway of the Precursor Form of Human Tripeptidyl-peptidase 1, the Enzyme Deficient in Late Infantile Ceroid Lipofuscinosis Authors: Guhaniyogi, J. / Sohar, I. / Das, K. / Stock, A.M. / Lobel, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3edy.cif.gz | 120.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3edy.ent.gz | 95.6 KB | Display | PDB format |
PDBx/mmJSON format | 3edy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/3edy ftp://data.pdbj.org/pub/pdb/validation_reports/ed/3edy | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 59369.121 Da / Num. of mol.: 1 / Fragment: residues 20-563 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TPP1, CLN2 / Cell (production host): OVARY CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O14773, tripeptidyl-peptidase I | ||||
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#2: Chemical | ChemComp-CA / | ||||
#3: Sugar | ChemComp-NAG / #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.85 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 6000, citrate, pH 5.0, vapor diffusion, hanging drop, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97908 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 2, 2007 / Details: mirrors |
Radiation | Monochromator: horizontally deflecting and focusing crystal preceded by a vertically focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97908 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→50 Å / Num. all: 48561 / Num. obs: 50890 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.079 / Χ2: 1.043 |
Reflection shell | Resolution: 1.83→1.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4675 / Χ2: 0.644 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Resolution: 1.85→29.72 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.187 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.871 / SU B: 5.22 / SU ML: 0.082 / SU R Cruickshank DPI: 0.141 / SU Rfree: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.134 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.13 Å2 / Biso mean: 26.882 Å2 / Biso min: 13.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→29.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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