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Yorodumi- PDB-7wgs: Structure of ClpP from Staphylococcus aureus in complex with (S)-ZG197 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wgs | ||||||||||||
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Title | Structure of ClpP from Staphylococcus aureus in complex with (S)-ZG197 | ||||||||||||
Components | ATP-dependent Clp protease proteolytic subunit | ||||||||||||
Keywords | HYDROLASE / ClpP / Staphyloccocus aureus / activator | ||||||||||||
Function / homology | Function and homology information endopeptidase Clp / ATP-dependent peptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||||||||
Authors | Yang, C.-G. / Gan, J.H. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Nat Commun / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wgs.cif.gz | 506.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wgs.ent.gz | 419 KB | Display | PDB format |
PDBx/mmJSON format | 7wgs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wgs_validation.pdf.gz | 4.5 MB | Display | wwPDB validaton report |
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Full document | 7wgs_full_validation.pdf.gz | 4.6 MB | Display | |
Data in XML | 7wgs_validation.xml.gz | 96.9 KB | Display | |
Data in CIF | 7wgs_validation.cif.gz | 126.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/7wgs ftp://data.pdbj.org/pub/pdb/validation_reports/wg/7wgs | HTTPS FTP |
-Related structure data
Related structure data | 7wh5C 7widC 7xbzC 3staS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Staphylococcus aureus (bacteria) / Gene: ClpP / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D1I3W4, endopeptidase Clp #2: Chemical | ChemComp-9A2 / ( #3: Chemical | ChemComp-MPD / ( #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.84 Å3/Da / Density % sol: 56.76 % |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→145.6 Å / Num. obs: 180268 / % possible obs: 97.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.11→2.22 Å / Rmerge(I) obs: 0.736 / Num. unique obs: 111 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3STA Resolution: 2.11→145.6 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.936 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.149 / 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: 122.84 Å2 / Biso mean: 40.685 Å2 / Biso min: 22.12 Å2
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Refinement step | Cycle: final / Resolution: 2.11→145.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.11→2.16 Å / Rfactor Rfree error: 0
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