+Open data
-Basic information
Entry | Database: PDB / ID: 4ifg | ||||||
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Title | Crystal structure of TgCDPK1 with inhibitor bound | ||||||
Components | Calmodulin-domain protein kinase 1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Structural Genomics / Structural Genomics Consortium / SGC / Kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information phosphorylation / protein serine/threonine kinase activity / calcium ion binding / ATP binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.11 Å | ||||||
Authors | El Bakkouri, M. / Tempel, W. / Crandall, I. / Massad, T. / Loppnau, P. / Graslund, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Kain, K. ...El Bakkouri, M. / Tempel, W. / Crandall, I. / Massad, T. / Loppnau, P. / Graslund, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Kain, K. / Hui, R. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of TgCDPK1 with inhibitor bound Authors: El Bakkouri, M. / Tempel, W. / Crandall, I. / Massad, T. / Loppnau, P. / Graslund, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Kain, K. / Hui, R. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ifg.cif.gz | 106.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ifg.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ifg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/4ifg ftp://data.pdbj.org/pub/pdb/validation_reports/if/4ifg | 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: 57333.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: CDPK1, TGGT1_059880, TGVEG_042030 / Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli) References: UniProt: Q9BJF5, Ca2+/calmodulin-dependent protein kinase |
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#2: Chemical | ChemComp-1E8 / |
#3: Chemical | ChemComp-UNX / |
#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: 2.02 Å3/Da / Density % sol: 39.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 25% PEG3350, 0.2M LiSO4, 0.1M Hepes pH 7.5, vapor diffusion, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97933 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.11→50 Å / Num. obs: 26339 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.069 / Χ2: 1.851 / Net I/σ(I): 12.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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Phasing MR | Packing: 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→48.82 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2738 / WRfactor Rwork: 0.2137 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.7849 / SU B: 6.832 / SU ML: 0.181 / SU R Cruickshank DPI: 0.2732 / SU Rfree: 0.2202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.273 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.02 Å2 / Biso mean: 53.9187 Å2 / Biso min: 27.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→48.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.106→2.161 Å / Total num. of bins used: 20
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