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Yorodumi- PDB-1k3b: Crystal Structure of Human Dipeptidyl Peptidase I (Cathepsin C): ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k3b | ||||||
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Title | Crystal Structure of Human Dipeptidyl Peptidase I (Cathepsin C): Exclusion Domain Added to an Endopeptidase Framework Creates the Machine for Activation of Granular Serine Proteases | ||||||
Components | (dipeptydil-peptidase I ...) x 3 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle ...dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle / phosphatase binding / cysteine-type peptidase activity / positive regulation of apoptotic signaling pathway / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / proteolysis involved in protein catabolic process / response to organic substance / T cell mediated cytotoxicity / : / azurophil granule lumen / protein-folding chaperone binding / collagen-containing extracellular matrix / lysosome / immune response / endoplasmic reticulum lumen / cysteine-type endopeptidase activity / serine-type endopeptidase activity / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD, MIR, MOL. REPL together / Resolution: 2.15 Å | ||||||
Authors | Turk, D. / Janjic, V. / Stern, I. / Podobnik, M. / Lamba, D. / Dahl, S.W. / Lauritzen, C. / Pedersen, J. / Turk, V. / Turk, B. | ||||||
Citation | Journal: EMBO J. / Year: 2001 Title: Structure of human dipeptidyl peptidase I (cathepsin C): exclusion domain added to an endopeptidase framework creates the machine for activation of granular serine proteases. Authors: Turk, D. / Janjic, V. / Stern, I. / Podobnik, M. / Lamba, D. / Dahl, S.W. / Lauritzen, C. / Pedersen, J. / Turk, V. / Turk, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k3b.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k3b.ent.gz | 71 KB | Display | PDB format |
PDBx/mmJSON format | 1k3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/1k3b ftp://data.pdbj.org/pub/pdb/validation_reports/k3/1k3b | 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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Details | tetramer molecule with tetrahaedral symmetry |
-Components
-Dipeptydil-peptidase I ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 13500.163 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): INSECT CELL(Invitrogen) / Cell line (production host): high five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53634, dipeptidyl-peptidase I |
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#2: Protein | Mass: 18491.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): INSECT CELL(Invitrogen) / Cell line (production host): high five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53634, dipeptidyl-peptidase I |
#3: Protein | Mass: 7583.444 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): INSECT CELL(Invitrogen) / Cell line (production host): high five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53634, dipeptidyl-peptidase I |
-Sugars , 1 types, 1 molecules
#4: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 468 molecules
#5: Chemical | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.7 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: ammonium sulphate, sodium citrate, potassium/sodium tartrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Jun 30, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→20 Å / Num. all: 23553 / Num. obs: 23553 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.07 |
Reflection shell | Resolution: 2.15→2.18 Å / Num. unique all: 23353 / Rsym value: 0.249 / % possible all: 0.99 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 96833 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 99 % / Rmerge(I) obs: 0.249 |
-Processing
Software |
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Refinement | Method to determine structure: MAD, MIR, MOL. REPL together / Resolution: 2.15→10 Å / Isotropic thermal model: isotropic / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 23.8 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→10 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rwork: 0.186 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |