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- PDB-7xbz: Crystal structure of Staphylococcus aureus ClpP in complex with R... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xbz | ||||||||||||
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Title | Crystal structure of Staphylococcus aureus ClpP in complex with R-ZG197 | ||||||||||||
![]() | ATP-dependent Clp protease proteolytic subunit | ||||||||||||
![]() | HYDROLASE / protease | ||||||||||||
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 | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Wei, B.Y. / Gan, J.H. / Yang, C.-G. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Anti-infective therapy using species-specific activators of Staphylococcus aureus ClpP. Authors: Wei, B. / Zhang, T. / Wang, P. / Pan, Y. / Li, J. / Chen, W. / Zhang, M. / Ji, Q. / Wu, W. / Lan, L. / Gan, J. / Yang, C.G. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 498 KB | Display | ![]() |
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PDB format | ![]() | 411.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4 MB | Display | ![]() |
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Full document | ![]() | 4 MB | Display | |
Data in XML | ![]() | 95.2 KB | Display | |
Data in CIF | ![]() | 123.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wgsC ![]() 7wh5C ![]() 7widC ![]() 3qwdS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 21536.531 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-D4E / ( #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-MPD / ( #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.86 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2M Sodium chloride, 0.1M Sodium acetate trihydrate pH 4.6, 30% v/v (+/-)-2-Methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 17, 2022 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.15→30 Å / Num. obs: 171564 / % possible obs: 94.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.06 / Rrim(I) all: 0.131 / Χ2: 1.426 / Net I/σ(I): 5.7 / Num. measured all: 618283 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3qwd Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.7 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.175 / 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: 113.15 Å2 / Biso mean: 37.684 Å2 / Biso min: 17.95 Å2
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Refinement step | Cycle: final / Resolution: 2.15→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.151→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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