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Yorodumi- PDB-1n6e: tricorn protease in complex with a tridecapeptide chloromethyl ke... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n6e | |||||||||
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Title | tricorn protease in complex with a tridecapeptide chloromethyl ketone derivative | |||||||||
Components |
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Keywords | HYDROLASE / tricorn protease / propeller | |||||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / proteolysis / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermoplasma acidophilum (acidophilic) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / direct refinement / Resolution: 2.6 Å | |||||||||
Authors | Kim, J.-S. / Groll, M. / Huber, R. / Brandstetter, H. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Navigation Inside a Protease: Substrate Selection and Product Exit in the Tricorn Protease from Thermoplasma acidophilum Authors: Kim, J.-S. / Groll, M. / Musiol, H.-J. / Behrendt, R. / Kaiser, M. / Moroder, L. / Huber, R. / Brandstetter, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n6e.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1n6e.ent.gz | 994.4 KB | Display | PDB format |
PDBx/mmJSON format | 1n6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/1n6e ftp://data.pdbj.org/pub/pdb/validation_reports/n6/1n6e | HTTPS FTP |
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-Related structure data
Related structure data | 1n6dC 1n6fC 1k32S S: Starting model for refinement C: citing same article (ref.) |
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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: 121779.531 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: tri, Ta1490 / Plasmid: pRSet6c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P96086, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Protein/peptide | Mass: 1503.073 Da / Num. of mol.: 6 / Source method: obtained synthetically Details: This sequence occurs naturally in thermoplasma acidophilum Source: (synth.) synthetic construct (others) #3: 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: 2.52 Å3/Da / Density % sol: 50.8 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: Isopropanol, MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
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: SLS / Beamline: X06SA / Wavelength: 0.9794 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 18, 2001 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 209855 / % possible obs: 97.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.07 % / Rsym value: 0.084 |
Reflection shell | Resolution: 2.6→2.64 Å / Rsym value: 0.305 / % possible all: 85.1 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 645775 / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS % possible obs: 85.1 % / Rmerge(I) obs: 0.305 |
-Processing
Software |
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Refinement | Method to determine structure: direct refinement Starting model: 1K32 Resolution: 2.6→6 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.6→6 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 8.6 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: n_bond_d / Dev ideal: 0.014 |