+Open data
-Basic information
Entry | Database: PDB / ID: 6kui | ||||||
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Title | Active conformation of HslV from Staphylococcus aureus. | ||||||
Components | ATP-dependent protease subunit HslV | ||||||
Keywords | HYDROLASE / HslV / bacterial proteasome / Threonine protease / protease | ||||||
Function / homology | Function and homology information HslU-HslV peptidase / HslUV protease complex / proteasome core complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Ha, N.-C. / Jeong, S. | ||||||
Citation | Journal: Mol.Cells / Year: 2020 Title: Cleavage-Dependent Activation of ATP-Dependent Protease HslUV from Staphylococcus aureus . Authors: Jeong, S. / Ahn, J. / Kwon, A.R. / Ha, N.-C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kui.cif.gz | 137.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kui.ent.gz | 86.3 KB | Display | PDB format |
PDBx/mmJSON format | 6kui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/6kui ftp://data.pdbj.org/pub/pdb/validation_reports/ku/6kui | HTTPS FTP |
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-Related structure data
Related structure data | 6kr1SC 6kwwC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 21636.568 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria) Gene: hslV, clpQ, SAV1253 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P65796, HslU-HslV peptidase #2: 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: 2.47 Å3/Da / Density % sol: 50.1 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris propane, Citric acid, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→50 Å / Num. obs: 27546 / % possible obs: 98.6 % / Redundancy: 8.7 % / Biso Wilson estimate: 26.65 Å2 / Rpim(I) all: 0.021 / Rrim(I) all: 0.073 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2.33→2.37 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1245 / Rpim(I) all: 0.184 / Rrim(I) all: 0.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KR1 Resolution: 2.33→41.25 Å / SU ML: 0.2976 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 23.4644
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33→41.25 Å
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Refine LS restraints |
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LS refinement shell |
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