+Open data
-Basic information
Entry | Database: PDB / ID: 1n6f | ||||||
---|---|---|---|---|---|---|---|
Title | tricorn protease in complex with Z-Phe-diketo-Arg-Glu-Phe | ||||||
Components | tricorn protease | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / direct refinement / Resolution: 2.7 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1n6f.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1n6f.ent.gz | 989.1 KB | Display | PDB format |
PDBx/mmJSON format | 1n6f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n6f_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1n6f_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 1n6f_validation.xml.gz | 242.4 KB | Display | |
Data in CIF | 1n6f_validation.cif.gz | 317.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/1n6f ftp://data.pdbj.org/pub/pdb/validation_reports/n6/1n6f | HTTPS FTP |
-Related structure data
Related structure data | 1n6dC 1n6eC 1k32S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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) / 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: Chemical | ChemComp-DKT / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.5 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 9, 2002 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. all: 295654 / Num. obs: 178808 / % possible obs: 93.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 1.65 % / Rsym value: 0.066 |
Reflection shell | Resolution: 2.7→2.75 Å / Rsym value: 0.263 / % possible all: 83.6 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 295654 / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 83.6 % / Rmerge(I) obs: 0.263 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: direct refinement Starting model: PDB entry 1K32 Resolution: 2.7→6 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→6 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 8.5 % / Rfactor Rfree: 0.28 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: n_bond_d / Dev ideal: 0.01 |