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- PDB-5vz2: Structure of ClpP from Staphylococcus aureus in complex with Acyl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vz2 | ||||||
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Title | Structure of ClpP from Staphylococcus aureus in complex with Acyldepsipeptide | ||||||
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![]() | HYDROLASE/ANTIBIOTIC / ClpP ADEP / HYDROLASE-ANTIBIOTIC complex | ||||||
Function / homology | ![]() endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Griffith, E.C. / Lee, R.E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Ureadepsipeptides as ClpP Activators. Authors: Griffith, E.C. / Zhao, Y. / Singh, A.P. / Conlon, B.P. / Tangallapally, R. / Shadrick, W.R. / Liu, J. / Wallace, M.J. / Yang, L. / Elmore, J.M. / Li, Y. / Zheng, Z. / Miller, D.J. / ...Authors: Griffith, E.C. / Zhao, Y. / Singh, A.P. / Conlon, B.P. / Tangallapally, R. / Shadrick, W.R. / Liu, J. / Wallace, M.J. / Yang, L. / Elmore, J.M. / Li, Y. / Zheng, Z. / Miller, D.J. / Cheramie, M.N. / Lee, R.B. / LaFleur, M.D. / Lewis, K. / Lee, R.E. #1: ![]() Title: Structural switching of Staphylococcus aureus Clp protease: a key to understanding protease dynamics. Authors: Zhang, J. / Ye, F. / Lan, L. / Jiang, H. / Luo, C. / Yang, C.G. #2: ![]() Title: Acyldepsipeptide antibiotics induce the formation of a structured axial channel in ClpP: A model for the ClpX/ClpA-bound state of ClpP. Authors: Li, D.H. / Chung, Y.S. / Gloyd, M. / Joseph, E. / Ghirlando, R. / Wright, G.D. / Cheng, Y.Q. / Maurizi, M.R. / Ortega, J. #3: ![]() Title: Insights into structural network responsible for oligomerization and activity of bacterial virulence regulator caseinolytic protease P (ClpP) protein. Authors: Gersch, M. / List, A. / Groll, M. / Sieber, S.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 500.4 KB | Display | ![]() |
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PDB format | ![]() | 412 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 577.2 KB | Display | ![]() |
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Full document | ![]() | 587.6 KB | Display | |
Data in XML | ![]() | 88.9 KB | Display | |
Data in CIF | ![]() | 125.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w18C ![]() 6pkaC ![]() 6pmdC ![]() 3staS 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: 22607.686 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: NCTC 8325 / Gene: clpP, SAOUHSC_00790 / Plasmid: pET28a / Production host: ![]() ![]() #2: Protein/peptide | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.14 % / Description: A 0.3 mm cube formed in 3 days at 18 C. |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1 M NaOAc pH 4.5, 18-35% MPD, and 0.02 M CaCl2 / PH range: 4.5-4.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 13, 2013 / Details: Mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.27→50 Å / Num. obs: 155067 / % possible obs: 97.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.067 / Χ2: 1.32 / Net I/σ(I): 10.8 / Num. measured all: 614075 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3STA Resolution: 2.26→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2108 / WRfactor Rwork: 0.1744 / FOM work R set: 0.8506 / SU B: 5.493 / SU ML: 0.137 / SU R Cruickshank DPI: 0.2203 / SU Rfree: 0.1834 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 119.15 Å2 / Biso mean: 37.633 Å2 / Biso min: 18 Å2
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Refinement step | Cycle: final / Resolution: 2.26→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.262→2.321 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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