[English] 日本語
Yorodumi- PDB-6aok: Crystal structure of Legionella pneumophila effector Ceg4 with N-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6aok | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Legionella pneumophila effector Ceg4 with N-terminal TEV protease cleavage 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 / SAD / Resolution: 1.88 Å | ||||||
Authors | Stogios, P.J. / Cuff, M.E. / Nocek, B. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6aok.cif.gz | 108.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6aok.ent.gz | 87.8 KB | Display | PDB format |
PDBx/mmJSON format | 6aok.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/6aok ftp://data.pdbj.org/pub/pdb/validation_reports/ao/6aok | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25616.592 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 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | #4: Chemical | ChemComp-TRS / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.12 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 0.2 M magnesium chloride, 0.5 mM manganese chloride, 0.1 M Tris pH 7.3, 30% (w/v) PEG 4K, 2 mM phosphotyrosine |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→40 Å / Num. obs: 16374 / % possible obs: 100 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.035 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.88→1.91 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 817 / CC1/2: 0.867 / Rpim(I) all: 0.266 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.88→37.172 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.55
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→37.172 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|