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- PDB-1n6e: tricorn protease in complex with a tridecapeptide chloromethyl ke... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1n6e | |||||||||
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Title | tricorn protease in complex with a tridecapeptide chloromethyl ketone derivative | |||||||||
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![]() | HYDROLASE / tricorn protease / propeller | |||||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / proteolysis / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Kim, J.-S. / Groll, M. / Huber, R. / Brandstetter, H. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 994.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 560.9 KB | Display | ![]() |
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Full document | ![]() | 739.5 KB | Display | |
Data in XML | ![]() | 232.6 KB | Display | |
Data in CIF | ![]() | 316.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1n6dC ![]() 1n6fC ![]() 1k32S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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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 |