+Open data
-Basic information
Entry | Database: PDB / ID: 4yga | ||||||
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Title | CDPK1, from Toxoplasma gondii, bound to inhibitory VHH-1B7 | ||||||
Components |
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Keywords | METAL BINDING PROTEIN / Serine/Threonine Protein Kinase / VHH Domain / Inhibitor | ||||||
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) Vicugna pacos (alpaca) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.94 Å | ||||||
Authors | Knockenhauer, K.E. / Schwartz, T.U. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Allosteric activation of apicomplexan calcium-dependent protein kinases. Authors: Ingram, J.R. / Knockenhauer, K.E. / Markus, B.M. / Mandelbaum, J. / Ramek, A. / Shan, Y. / Shaw, D.E. / Schwartz, T.U. / Ploegh, H.L. / Lourido, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yga.cif.gz | 898.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yga.ent.gz | 769.2 KB | Display | PDB format |
PDBx/mmJSON format | 4yga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/4yga ftp://data.pdbj.org/pub/pdb/validation_reports/yg/4yga | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 58535.398 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: CDPK1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)V2RpAcYc-LIC+LamP / References: UniProt: Q9BJF5 #2: Antibody | Mass: 15442.187 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-LOBSTR-RIL #3: Chemical | ChemComp-CA / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% w/v PEG 3350, 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 6.5, 4% v/v 1-propanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.94→73.04 Å / Num. obs: 53985 / % possible obs: 93.5 % / Redundancy: 3.9 % / Rsym value: 0.11 / Net I/σ(I): 10.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.94→70.67 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 33.11 / 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: 2.94→70.67 Å
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Refine LS restraints |
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LS refinement shell |
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