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Yorodumi- PDB-5t6i: CRYSTAL STRUCTURE OF TGCDPK1 FROM TOXOPLASMA GONDII COMPLEXED WITH 5GB -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t6i | |||||||||
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Title | CRYSTAL STRUCTURE OF TGCDPK1 FROM TOXOPLASMA GONDII COMPLEXED WITH 5GB | |||||||||
Components | Calmodulin-domain protein kinase 1 | |||||||||
Keywords | TRANSFERASE / Structural Genomics Consortium / SGC / CDPks / Serine/Threonine Protein Kinase / Nucleotide-Binding | |||||||||
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 / FOURIER SYNTHESIS / Resolution: 2.05 Å | |||||||||
Authors | Jiang, D.Q. / Tempel, W. / Walker, J.R. / El Bakkouri, M. / Loppnau, P. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. ...Jiang, D.Q. / Tempel, W. / Walker, J.R. / El Bakkouri, M. / Loppnau, P. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Lovato, D.V. / Osman, K.T. / Structural Genomics Consortium (SGC) | |||||||||
Citation | Journal: to be published Title: Crystal Structure of CDPK1 from toxoplasma gondii complexed with SGC-1-19 Authors: Jiang, D.Q. / Tempel, W. / Walker, J.R. / El Bakkouri, M. / Loppnau, P. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Lovato, D.V. / Osman, K.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t6i.cif.gz | 189.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t6i.ent.gz | 147.3 KB | Display | PDB format |
PDBx/mmJSON format | 5t6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/5t6i ftp://data.pdbj.org/pub/pdb/validation_reports/t6/5t6i | HTTPS FTP |
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-Related structure data
Related structure data | 5t6kC 3ku2S 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
#1: Protein | Mass: 59533.410 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(DE3) / References: UniProt: Q9BJF5 |
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#2: Chemical | ChemComp-5GB / |
#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: 1.92 Å3/Da / Density % sol: 35.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 3350, DI SODIUM-TART, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→72.49 Å / Num. obs: 27889 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 48.33 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.054 / Mean I/σ(I) obs: 1.4 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3KU2 Resolution: 2.05→31.71 Å / Cor.coef. Fo:Fc: 0.9489 / Cor.coef. Fo:Fc free: 0.9368 / SU R Cruickshank DPI: 0.662 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.199 / SU Rfree Blow DPI: 0.16 / SU Rfree Cruickshank DPI: 0.163 Details: THIS STRUCTURE MODEL WAS REFINED AND ADJUSTED USING 3KU2, A STRUCTURE MODEL OF THE SAME PROTEIN COMPLEXED WITH ANP, AS A TEMPLATE. THERE ARE GAPS IN THE PROTEIN CHAIN AND ALSO POORLY ...Details: THIS STRUCTURE MODEL WAS REFINED AND ADJUSTED USING 3KU2, A STRUCTURE MODEL OF THE SAME PROTEIN COMPLEXED WITH ANP, AS A TEMPLATE. THERE ARE GAPS IN THE PROTEIN CHAIN AND ALSO POORLY RESOLVED LOOPS WHICH ARE EASY TO MISINTERPRET. WHOEVER ANALYZES THE STRUCTURE NEEDS TO CONSIDER THE RISK OF OUT-OF-REGISTER ERRORS UNDER THESE CIRCUMSTANCES, AND IS RECOMMENDED TO REFER TO THE ELECTRON DENSITY MAP FOR MODEL CREDIBILITY.
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Displacement parameters | Biso mean: 66.49 Å2
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Refine analyze | Luzzati coordinate error obs: 0.292 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→31.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.13 Å / Total num. of bins used: 14
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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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