+Open data
-Basic information
Entry | Database: PDB / ID: 6kr1 | ||||||
---|---|---|---|---|---|---|---|
Title | ATP dependent protease HslV from Staphylococcus aureus | ||||||
Components | ATP-dependent protease subunit HslV | ||||||
Keywords | HYDROLASE / Threonine prtease / HslUV / bacterial proteasome | ||||||
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 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6kr1.cif.gz | 507.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6kr1.ent.gz | 337.3 KB | Display | PDB format |
PDBx/mmJSON format | 6kr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kr1_validation.pdf.gz | 536.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6kr1_full_validation.pdf.gz | 552.8 KB | Display | |
Data in XML | 6kr1_validation.xml.gz | 79.5 KB | Display | |
Data in CIF | 6kr1_validation.cif.gz | 110.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/6kr1 ftp://data.pdbj.org/pub/pdb/validation_reports/kr/6kr1 | HTTPS FTP |
-Related structure data
Related structure data | 6kuiC 6kwwC 1yyfS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
4 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20703.564 Da / Num. of mol.: 12 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: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.65 % |
---|---|
Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES:NaOH, Lithium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 150435 / % possible obs: 98.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 23.48 Å2 / Rpim(I) all: 0.028 / Rrim(I) all: 0.082 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7367 / Rpim(I) all: 0.26 / Rrim(I) all: 0.526 / % possible all: 96.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YYF Resolution: 2→33.16 Å / SU ML: 0.3074 / Cross valid method: FREE R-VALUE / σ(F): 2.18 / Phase error: 27.4435 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→33.16 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|