+Open data
-Basic information
Entry | Database: PDB / ID: 5clr | ||||||
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Title | Crystal structure of LegK4_APO Kinase | ||||||
Components | LegK4 | ||||||
Keywords | TRANSFERASE / Legionella / Bacterial effectors / serine/threonine kinase / type IV secretion system | ||||||
Function / homology | Function and homology information non-specific serine/threonine protein kinase / protein phosphorylation / protein serine/threonine kinase activity / ATP binding Similarity search - Function | ||||||
Biological species | Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.706 Å | ||||||
Authors | Flayhan, A. / Terradot, L. | ||||||
Citation | Journal: Sci Rep / Year: 2015 Title: The structure of Legionella pneumophila LegK4 type four secretion system (T4SS) effector reveals a novel dimeric eukaryotic-like kinase. Authors: Flayhan, A. / Berge, C. / Bailo, N. / Doublet, P. / Bayliss, R. / Terradot, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5clr.cif.gz | 291.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5clr.ent.gz | 248.1 KB | Display | PDB format |
PDBx/mmJSON format | 5clr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/5clr ftp://data.pdbj.org/pub/pdb/validation_reports/cl/5clr | HTTPS FTP |
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-Related 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: 51578.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (strain Lens) (bacteria) Gene: lpl0262 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5WZW9 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12% (w/v) PEG 4000, 20% glycerol, 0.1 M MOPS/HEPES pH 7.5, 5 mM Hexaammine cobalt (III) chloride. |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2013 |
Radiation | Monochromator: si [111] crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→44.693 Å / Num. obs: 13215 / % possible obs: 100 % / Redundancy: 11 % / Rmerge(I) obs: 0.239 / Net I/σ(I): 13.79 |
Reflection shell | Resolution: 3.706→3.838 Å / Redundancy: 2.47 % / Rmerge(I) obs: 1.419 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.706→44.693 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.706→44.693 Å
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Refine LS restraints |
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LS refinement shell |
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