[English] 日本語
Yorodumi- PDB-4emp: Crystal structure of the mutant of ClpP E137A from Staphylococcus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4emp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the mutant of ClpP E137A from Staphylococcus aureus | ||||||
Components | ATP-dependent Clp protease proteolytic subunit | ||||||
Keywords | HYDROLASE / tetradecameric chamber / ATP-dependent Clp protease proteolytic subunit / protein binding | ||||||
Function / homology | Function and homology information endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Ye, F. / Zhang, J. / Liu, H. / Luo, C. / Yang, C.-G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Helix unfolding/refolding characterizes the functional dynamics of Staphylococcus aureus Clp protease Authors: Ye, F. / Zhang, J. / Liu, H. / Hilgenfeld, R. / Zhang, R. / Kong, X. / Li, L. / Lu, J. / Zhang, X. / Li, D. / Jiang, H. / Yang, C.-G. / Luo, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4emp.cif.gz | 477.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4emp.ent.gz | 395 KB | Display | PDB format |
PDBx/mmJSON format | 4emp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4emp_validation.pdf.gz | 547.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4emp_full_validation.pdf.gz | 601.6 KB | Display | |
Data in XML | 4emp_validation.xml.gz | 85.7 KB | Display | |
Data in CIF | 4emp_validation.cif.gz | 115.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/4emp ftp://data.pdbj.org/pub/pdb/validation_reports/em/4emp | HTTPS FTP |
-Related structure data
Related structure data | 4emmC 3staS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21889.949 Da / Num. of mol.: 14 / Mutation: E137A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MW2 / Gene: clpP / Production host: Escherichia coli (E. coli) / References: UniProt: P63786, endopeptidase Clp #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.65 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100mM BIS-TRIS, 2.0M ammonium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 5, 2011 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 92694 / Num. obs: 88480 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.6→2.69 Å / % possible all: 98.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3STA Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.878 / SU B: 14.818 / SU ML: 0.306 / Cross valid method: THROUGHOUT / σ(F): 4 / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.411 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
|