+Open data
-Basic information
Entry | Database: PDB / ID: 5w9e | ||||||
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Title | Toxoplasma Gondii CDPK1 in complex with inhibitor GXJ-186 | ||||||
Components | Calmodulin-domain protein kinase 1 | ||||||
Keywords | transferase/transferase inhibitor / CDPK / PARASITOLOGY / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / TRANSFERASE / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information calcium-dependent protein serine/threonine kinase activity / calmodulin-dependent protein kinase activity / calmodulin binding / intracellular signal transduction / phosphorylation / calcium ion binding / ATP binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.44 Å | ||||||
Authors | El Bakkouri, M. / Lovato, D. / Loppnau, P. / Lin, Y.H. / Rutaganaria, F. / Lopez, M.S. / Shokat, L. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. ...El Bakkouri, M. / Lovato, D. / Loppnau, P. / Lin, Y.H. / Rutaganaria, F. / Lopez, M.S. / Shokat, L. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Sibley, D. / Hui, R. / Walker, J.R. | ||||||
Citation | Journal: To be published Title: Toxoplasma Gondii CDPK1 in complex with inhibitor GXJ-186 Authors: El Bakkouri, M. / Lovato, D. / Loppnau, P. / Lin, Y.H. / Rutaganaria, F. / Lopez, M.S. / Shokat, L. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Sibley, D. / Hui, R. / Walker, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w9e.cif.gz | 192.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w9e.ent.gz | 152.4 KB | Display | PDB format |
PDBx/mmJSON format | 5w9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/5w9e ftp://data.pdbj.org/pub/pdb/validation_reports/w9/5w9e | HTTPS FTP |
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-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: 55226.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: CDPK1 / Plasmid: PET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9BJF5 |
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#2: Chemical | ChemComp-9YJ / |
#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: 2.02 Å3/Da / Density % sol: 39.15 % / Mosaicity: 0.53 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% PEG8K, 0.2M NaCl, 0.1M Hepes pH7.5, 5 % Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2015 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.44→48.01 Å / Num. obs: 16313 / Biso Wilson estimate: 56.93 Å2 | ||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.4 %
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-Processing
Software |
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Refinement | Resolution: 2.44→48.01 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.901 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.637 / SU Rfree Blow DPI: 0.278
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Displacement parameters | Biso mean: 62.54 Å2
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Refine analyze | Luzzati coordinate error obs: 0.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.44→48.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.44→2.61 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
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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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