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Yorodumi- PDB-6r50: Crystal structure of holo PPEP-1(E143A/Y178F) in complex with sub... -
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-Basic information
Entry | Database: PDB / ID: 6r50 | ||||||
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Title | Crystal structure of holo PPEP-1(E143A/Y178F) in complex with substrate peptide Ac-EVNAPVP-CONH2 | ||||||
Components |
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Keywords | HYDROLASE / Pro-Pro endopeptidase 1 / zinc metallopeptidase / Clostridium difficile / virulence factor | ||||||
Function / homology | Function and homology information Pro-Pro endopeptidase / metallopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Peptoclostridium difficile (bacteria) Clostridioides difficile (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.807 Å | ||||||
Authors | Pichlo, C. / Baumann, U. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Molecular determinants of the mechanism and substrate specificity ofClostridium difficileproline-proline endopeptidase-1. Authors: Pichlo, C. / Juetten, L. / Wojtalla, F. / Schacherl, M. / Diaz, D. / Baumann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r50.cif.gz | 246.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r50.ent.gz | 201.1 KB | Display | PDB format |
PDBx/mmJSON format | 6r50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r50_validation.pdf.gz | 427.2 KB | Display | wwPDB validaton report |
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Full document | 6r50_full_validation.pdf.gz | 427.4 KB | Display | |
Data in XML | 6r50_validation.xml.gz | 20 KB | Display | |
Data in CIF | 6r50_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/6r50 ftp://data.pdbj.org/pub/pdb/validation_reports/r5/6r50 | HTTPS FTP |
-Related structure data
Related structure data | 6r4wC 6r4xC 6r4yC 6r4zC 6r51C 6r52C 6r53C 6r54C 6r55C 6r56C 6r57C 6r58C 6r59C 6r5aC 6r5bC 6r5cC 6r9zC 5a0pS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21909.646 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Peptoclostridium difficile / Gene: zmp1, ppep-1, CD630_28300 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q183R7, Pro-Pro endopeptidase #2: Protein/peptide | Mass: 749.855 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria) #3: Chemical | #4: 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: 2.21 Å3/Da / Density % sol: 44.42 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 1 microl 12 mg per ml rPPEP-1 E143A Y178F with 6 mM substrate peptide in 20 mM Tris pH 7.5, 200 mM NaCl, 0.1 mM ZnCl2 was mixed with 2 microl precipitant solution containing: 100 mM Tris pH ...Details: 1 microl 12 mg per ml rPPEP-1 E143A Y178F with 6 mM substrate peptide in 20 mM Tris pH 7.5, 200 mM NaCl, 0.1 mM ZnCl2 was mixed with 2 microl precipitant solution containing: 100 mM Tris pH 7.5, 2.25 M ammonium phosphate dibasic. Reservoir volume: 200 microl |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.807→40.93 Å / Num. obs: 35979 / % possible obs: 99 % / Redundancy: 3.4 % / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.81→1.87 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5A0P Resolution: 1.807→40.926 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 16.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.807→40.926 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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