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Yorodumi- PDB-1fd9: CRYSTAL STRUCTURE OF THE MACROPHAGE INFECTIVITY POTENTIATOR PROTE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fd9 | ||||||
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Title | CRYSTAL STRUCTURE OF THE MACROPHAGE INFECTIVITY POTENTIATOR PROTEIN (MIP) A MAJOR VIRULENCE FACTOR FROM LEGIONELLA PNEUMOPHILA | ||||||
Components | PROTEIN (MACROPHAGE INFECTIVITY POTENTIATOR PROTEIN) | ||||||
Keywords | ISOMERASE / FKBP DOMAIN / LONG ALPHA HELIX / DIMERISATION VIA HELICAL INTERACTIONS | ||||||
Function / homology | Function and homology information : / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cell outer membrane / protein folding Similarity search - Function | ||||||
Biological species | Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.41 Å | ||||||
Authors | Riboldi-Tunnicliffe, A. / Jessen, S. / Konig, B. / Rahfeld, J. / Hacker, J. / Fischer, G. / Hilgenfeld, R. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Crystal structure of Mip, a prolylisomerase from Legionella pneumophila Authors: Riboldi-Tunnicliffe, A. / Konig, B. / Jessen, S. / Weiss, M.S. / Rahfeld, J. / Hacker, J. / Fischer, G. / Hilgenfeld, R. #1: Journal: Mol.Microbiol. / Year: 1992 Title: Mip protein of Legionella pneumophila exhibits peptidyl-prolyl-cis/trans isomerase (PPlase) activity. Authors: Fischer, G. / Bang, H. / Ludwig, B. / Mann, K. / Hacker, J. #2: Journal: FEMS Microbiol.Rev. / Year: 1994 Title: Characterization of Mip proteins of Legionella pneumophila. Authors: Ludwig, B. / Rahfeld, J. / Schmidt, B. / Mann, K. / Wintermeyer, E. / Fischer, G. / Hacker, J. #3: Journal: FEBS Lett. / Year: 1995 Title: Small angle X-ray solution scattering study on the dimerization of the FKBP25mem from Legionella pneumophila Authors: Schmidt, B. / Konig, S. / Svergun, D. / Volkov, V. / Fischer, G. / Koch, M.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fd9.cif.gz | 54 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fd9.ent.gz | 38.9 KB | Display | PDB format |
PDBx/mmJSON format | 1fd9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fd9_validation.pdf.gz | 367.1 KB | Display | wwPDB validaton report |
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Full document | 1fd9_full_validation.pdf.gz | 371.7 KB | Display | |
Data in XML | 1fd9_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 1fd9_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/1fd9 ftp://data.pdbj.org/pub/pdb/validation_reports/fd/1fd9 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22869.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Plasmid: PBLL106 / Production host: Escherichia coli (E. coli) References: UniProt: P69059, UniProt: Q5ZXE0*PLUS, peptidylprolyl isomerase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8,000, zinc acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.279 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 2, 1998 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.279 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→22.4 Å / Num. obs: 13545 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 2.58 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.075 / Net I/σ(I): 2.7 |
Reflection shell | Resolution: 2.41→2.55 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.23 / % possible all: 88.2 |
Reflection | *PLUS Highest resolution: 2.41 Å / Lowest resolution: 22.4 Å / Num. obs: 10976 / % possible obs: 99.4 % / Redundancy: 4.8 % / Num. measured all: 52836 / Rmerge(I) obs: 0.103 |
Reflection shell | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 2.69 Å / % possible obs: 99.7 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 3.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.41→22.4 Å / Rfactor Rfree error: 0.009 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 84.82 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.41→22.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.41 Å / Lowest resolution: 22.4 Å / Num. reflection obs: 13169 / σ(F): 0 / Num. reflection Rfree: 1055 / % reflection Rfree: 8 % / Rfactor Rfree: 0.2805 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 59.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.303 / % reflection Rfree: 8.1 % / Rfactor Rwork: 0.257 |