+Open data
-Basic information
Entry | Database: PDB / ID: 2df5 | ||||||
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Title | Crystal Structure of Pf-PCP(1-204)-C | ||||||
Components | Pyrrolidone-carboxylate peptidase | ||||||
Keywords | HYDROLASE / Chameleon sequence / Pyrococcus furiosus / Pyrrolidone carboxyl peptidase | ||||||
Function / homology | Function and homology information pyroglutamyl-peptidase I / pyroglutamyl-peptidase activity / proteolysis / cytosol Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Katagiri, Y. / Takano, K. / Chon, H. / Matsumura, H. / Koga, Y. / Kanaya, S. | ||||||
Citation | Journal: Proteins / Year: 2007 Title: Conformational contagion in a protein: structural properties of a chameleon sequence Authors: Takano, K. / Katagiri, Y. / Mukaiyama, A. / Chon, H. / Matsumura, H. / Koga, Y. / Kanaya, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2df5.cif.gz | 178.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2df5.ent.gz | 143.8 KB | Display | PDB format |
PDBx/mmJSON format | 2df5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2df5_validation.pdf.gz | 453.1 KB | Display | wwPDB validaton report |
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Full document | 2df5_full_validation.pdf.gz | 471.3 KB | Display | |
Data in XML | 2df5_validation.xml.gz | 37.7 KB | Display | |
Data in CIF | 2df5_validation.cif.gz | 53.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/2df5 ftp://data.pdbj.org/pub/pdb/validation_reports/df/2df5 | HTTPS FTP |
-Related structure data
Related structure data | 2dfeC 2dffC 2dfhC 2dfiC 1iofS 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: 23387.379 Da / Num. of mol.: 4 / Mutation: chameleon sequece Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: pPCP3-C01 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: O73944, pyroglutamyl-peptidase I #2: Water | ChemComp-HOH / | Sequence details | THESE ARE CHAMELEON SEQUENCE | |
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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: 2.76 Å3/Da / Density % sol: 55.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 2.0M Ammonium sulfate, 5%(v/v) iso-propanol, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Dec 8, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 44050 / % possible obs: 98.2 % / Biso Wilson estimate: 15.5 Å2 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 89.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1IOF Resolution: 2.3→29.24 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 848754.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.535 Å2 / ksol: 0.365764 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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