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Yorodumi- PDB-2zl4: Crystal structure of H.pylori ClpP S99A in complex with the pepti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zl4 | ||||||
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Title | Crystal structure of H.pylori ClpP S99A in complex with the peptide AAAA | ||||||
Components |
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Keywords | HYDROLASE / peptide substrate / tetra-ala / Cytoplasm / Protease / Serine protease | ||||||
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 / cytoplasm Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kim, D.Y. / Kim, K.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: The structural basis for the activation and peptide recognition of bacterial ClpP Authors: Kim, D.Y. / Kim, K.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zl4.cif.gz | 465.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zl4.ent.gz | 385.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zl4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zl4_validation.pdf.gz | 591.7 KB | Display | wwPDB validaton report |
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Full document | 2zl4_full_validation.pdf.gz | 639.6 KB | Display | |
Data in XML | 2zl4_validation.xml.gz | 90.5 KB | Display | |
Data in CIF | 2zl4_validation.cif.gz | 123.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/2zl4 ftp://data.pdbj.org/pub/pdb/validation_reports/zl/2zl4 | HTTPS FTP |
-Related structure data
Related structure data | 2zl0SC 2zl2C 2zl3C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21531.674 Da / Num. of mol.: 14 / Mutation: S99A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: clpP / Plasmid: pET-22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P56156, endopeptidase Clp #2: Protein/peptide | Mass: 302.326 Da / Num. of mol.: 14 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. #3: Water | ChemComp-HOH / | |
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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: 2.35 Å3/Da / Density % sol: 47.61 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 7.5 Details: 32% PEG400, 0.1M HEPES, 0.35M magnesium chloride, pH 7.5, Microbatch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 25, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 101077 / Biso Wilson estimate: 32.2 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZL0 Resolution: 2.5→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 5575528.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.7551 Å2 / ksol: 0.45 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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