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- PDB-6r57: Crystal structure of PPEP-1(E143A/Y178F/E184A) in complex with su... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6r57 | ||||||
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Title | Crystal structure of PPEP-1(E143A/Y178F/E184A) in complex with substrate peptide Ac-EVNPPVP-CONH2 | ||||||
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![]() | HYDROLASE / Pro-Pro endopeptidase 1 / zinc metallopeptidase / Clostridium difficile / virulence factor | ||||||
Function / homology | ![]() Pro-Pro endopeptidase / metallopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pichlo, C. / Baumann, U. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 242.3 KB | Display | ![]() |
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PDB format | ![]() | 198 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6r4wC ![]() 6r4xC ![]() 6r4yC ![]() 6r4zC ![]() 6r50C ![]() 6r51C ![]() 6r52C ![]() 6r53C ![]() 6r54C ![]() 6r55C ![]() 6r56C ![]() 6r58C ![]() 6r59C ![]() 6r5aC ![]() 6r5bC ![]() 6r5cC ![]() 6r9zC ![]() 5a0pS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21851.611 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 775.892 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | ChemComp-ZN / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.53 % |
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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 E184A in 6 mM substrate peptide in 20 mM Tris pH 7.5, 200 mM NaCl was mixed with 2 microl precipitant solution containing: 100 mM Tris pH 9.0, 2.25 ...Details: 1 microl 12 mg per ml rPPEP-1 E143A Y178F E184A in 6 mM substrate peptide in 20 mM Tris pH 7.5, 200 mM NaCl was mixed with 2 microl precipitant solution containing: 100 mM Tris pH 9.0, 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: ![]() ![]() ![]() |
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: 1.899→40.525 Å / Num. obs: 30422 / % possible obs: 99.42 % / Redundancy: 3.4 % / Net I/σ(I): 12.92 |
Reflection shell | Resolution: 1.899→1.967 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5A0P Resolution: 1.899→40.52 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 18.95
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.899→40.52 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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