+Open data
-Basic information
Entry | Database: PDB / ID: 3hzt | ||||||
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Title | Crystal structure of Toxoplasma gondii CDPK3, TGME49_105860 | ||||||
Components | Calcium-dependent protein kinase 3 | ||||||
Keywords | TRANSFERASE / calcium dependent kinase / calmodulin / troponin parasite / Structural Genomics / Structural Genomics Consortium / SGC / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase | ||||||
Function / homology | Function and homology information protein kinase activity / 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 Å | ||||||
Authors | Wernimont, A.K. / Artz, J.D. / Finnerty, P. / Wasney, G. / Allali-Hassani, A. / Vedadi, M. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Wernimont, A.K. / Artz, J.D. / Finnerty, P. / Wasney, G. / Allali-Hassani, A. / Vedadi, M. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Amani, M. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Structures of apicomplexan calcium-dependent protein kinases reveal mechanism of activation by calcium. Authors: Wernimont, A.K. / Artz, J.D. / Finerty, P. / Lin, Y.H. / Amani, M. / Allali-Hassani, A. / Senisterra, G. / Vedadi, M. / Tempel, W. / Mackenzie, F. / Chau, I. / Lourido, S. / Sibley, L.D. / Hui, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hzt.cif.gz | 108.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hzt.ent.gz | 79.4 KB | Display | PDB format |
PDBx/mmJSON format | 3hzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/3hzt ftp://data.pdbj.org/pub/pdb/validation_reports/hz/3hzt | HTTPS FTP |
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-Related structure data
Related structure data | 3hx4C 3igoC 3ku2C 3dxnS C: citing same article (ref.) S: Starting model for refinement |
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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: 53426.926 Da / Num. of mol.: 1 / Fragment: UNP residues 72-537 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: ME49 / Gene: TGME49_105860 / Plasmid: pET15_mhl / Production host: Escherichia coli (E. coli) References: UniProt: B6KR85, UniProt: Q3HNM6*PLUS, Ca2+/calmodulin-dependent protein kinase | ||||
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#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-J60 / | #5: 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: 2.45 Å3/Da / Density % sol: 49.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18% PEG 3350, 0.2 M KF, 3 mM SU11652, Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 35409 / Num. obs: 35409 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.033 / Χ2: 1.12 / Net I/σ(I): 26.63 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.686 / Num. unique all: 1693 / Rsym value: 0.369 / Χ2: 1.273 / % possible all: 96.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3DXN Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.207 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.829 / SU B: 4.157 / SU ML: 0.118 / SU R Cruickshank DPI: 0.185 / SU Rfree: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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: 93.18 Å2 / Biso mean: 42.411 Å2 / Biso min: 13.87 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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