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Yorodumi- PDB-6aoj: Crystal structure of Legionella pneumophila effector Ceg4 with N-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6aoj | ||||||
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Title | Crystal structure of Legionella pneumophila effector Ceg4 with N-terminal yeast Hog1p sequence | ||||||
Components | Ceg4 | ||||||
Keywords | HYDROLASE / Effector / Legionella pneumophila / infection / HAD-like phosphatase / alpha/beta protein / phosphotyrosine | ||||||
Function / homology | HAD-like superfamily / membrane / Dot/Icm T4SS effector Function and homology information | ||||||
Biological species | Legionella pneumophila subsp. pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å | ||||||
Authors | Stogios, P.J. / Nocek, B. / Cuff, M.E. / Evdokimova, E. / Egorova, O. / Yim, V. / Di Leo, R. / Savchenko, A. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: TheLegionella pneumophilaeffector Ceg4 is a phosphotyrosine phosphatase that attenuates activation of eukaryotic MAPK pathways. Authors: Quaile, A.T. / Stogios, P.J. / Egorova, O. / Evdokimova, E. / Valleau, D. / Nocek, B. / Kompella, P.S. / Peisajovich, S. / Yakunin, A.F. / Ensminger, A.W. / Savchenko, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6aoj.cif.gz | 110.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aoj.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 6aoj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/6aoj ftp://data.pdbj.org/pub/pdb/validation_reports/ao/6aoj | HTTPS FTP |
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-Related structure data
Related structure data | 6aokSC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 24925.596 Da / Num. of mol.: 1 / Fragment: UNP residues 1-208 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg0096 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q5ZZB5 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-CL / |
#4: 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: 2.79 Å3/Da / Density % sol: 55.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M sodium chloride, 0.1 M bis-Tris pH 6.5, 25% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 20881 / % possible obs: 97.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.031 / Net I/σ(I): 39.3 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 992 / CC1/2: 0.961 / Rpim(I) all: 0.149 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6AOK Resolution: 1.902→32.529 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.902→32.529 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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