+Open data
-Basic information
Entry | Database: PDB / ID: 2dfi | ||||||
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Title | Crystal structure of Pf-MAP(1-292)-C | ||||||
Components | Methionine aminopeptidaseMethionyl aminopeptidase | ||||||
Keywords | HYDROLASE / Chameleon sequence / fusion protein / Methionine aminopeptidase / Pyrococcus furiosus / Pf-MAP | ||||||
Function / homology | Function and homology information initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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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Remark 999 | SEQUENCE These are chameleon sequence |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dfi.cif.gz | 133.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dfi.ent.gz | 104.2 KB | Display | PDB format |
PDBx/mmJSON format | 2dfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/2dfi ftp://data.pdbj.org/pub/pdb/validation_reports/df/2dfi | HTTPS FTP |
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-Related structure data
Related structure data | 2df5C 2dfeC 2dffC 2dfhC 1xgmS 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: 33577.199 Da / Num. of mol.: 2 / Mutation: chameleon sequence Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: map / Plasmid: pMAP-C01 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P56218, methionyl aminopeptidase #2: Chemical | ChemComp-CO / #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: 2.08 Å3/Da / Density % sol: 40.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% Ethanol, 0.1M Tris-HCl, 20% PEG600, pH 8.5, 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: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 31, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 36807 / % possible obs: 98.8 % / Biso Wilson estimate: 12.2 Å2 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 90.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XGM Resolution: 2.1→46.19 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1126080.43 / 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: 56.2126 Å2 / ksol: 0.398849 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→46.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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