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Yorodumi- PDB-3nyv: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nyv | ||||||
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Title | Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with non-specific inhibitor WHI-P180 | ||||||
Components | Calmodulin-domain protein kinase 1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / serine/threonine protein kinase / transferase / calcium-binding / ATP-binding / calmodulin / EF hand / bumped kinase inhibitor / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP / 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 / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.88 Å | ||||||
Authors | Larson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP) | ||||||
Citation | Journal: To be Published Title: Binding modes of non-specific inhibitors of Calcium-Dependent Protein Kinase 1 (CDPK1) from T. gondii and C. parvum Authors: Larson, E.T. / Ojo, K.K. / Kim, J.E. / Verlinde, C.L.M.J. / Buckner, F.S. / Hol, W.G.J. / Merritt, E.A. / Van Voorhis, W.C. #1: Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Toxoplasma gondii calcium-dependent protein kinase 1 is a target for selective kinase inhibitors Authors: Ojo, K.K. / Larson, E.T. / Keyloun, K.R. / Castaneda, L.J. / Derocher, A.E. / Inampudi, K.K. / Kim, J.E. / Arakaki, T.L. / Murphy, R.C. / Zhang, L. / Napuli, A.J. / Maly, D.J. / Verlinde, C. ...Authors: Ojo, K.K. / Larson, E.T. / Keyloun, K.R. / Castaneda, L.J. / Derocher, A.E. / Inampudi, K.K. / Kim, J.E. / Arakaki, T.L. / Murphy, R.C. / Zhang, L. / Napuli, A.J. / Maly, D.J. / Verlinde, C.L. / Buckner, F.S. / Parsons, M. / Hol, W.G. / Merritt, E.A. / Van Voorhis, W.C. #2: Journal: ACS Med.Chem.Lett. / Year: 2010 Title: Discovery of potent and selective inhibitors of CDPK1 from C. parvum and T. gondii Authors: Murphy, R.C. / Ojo, K.K. / Larson, E.T. / Castellanos-Gonzalez, A. / Perera, B.G.K. / Keyloun, K.R. / Kim, J.E. / Bhandari, J.G. / Muller, N. / Verlinde, C.L.M.J. / Nakazawa, S.H. / Hol, W.G. ...Authors: Murphy, R.C. / Ojo, K.K. / Larson, E.T. / Castellanos-Gonzalez, A. / Perera, B.G.K. / Keyloun, K.R. / Kim, J.E. / Bhandari, J.G. / Muller, N. / Verlinde, C.L.M.J. / Nakazawa, S.H. / Hol, W.G.J. / Buckner, F.S. / Napuli, A.J. / White, C.A. / Merritt, E.A. / Van Voorhis, W.C. / Maly, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nyv.cif.gz | 205.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nyv.ent.gz | 163.4 KB | Display | PDB format |
PDBx/mmJSON format | 3nyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/3nyv ftp://data.pdbj.org/pub/pdb/validation_reports/ny/3nyv | HTTPS FTP |
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-Related structure data
Related structure data | 3i7cS 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: 55977.227 Da / Num. of mol.: 1 / Fragment: TgCDPK1, residues 30-507 Source method: isolated from a genetically manipulated source Details: residues 1-29 were replaced with a 3C cleavable His-tag; tag was cleaved prior to crystallization Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: AAG53993, CDPK1 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9BJF5, Ca2+/calmodulin-dependent protein kinase |
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#2: Chemical | ChemComp-DTQ / |
#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: 2.04 Å3/Da / Density % sol: 39.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 27% PEG 3350, 0.275 M ammonium citrate, 5 mM DTT, 2.3 mM WHI-P180; frozen directly in LN2, pH 6.5, vapor diffusion, sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 18, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.88→50 Å / Num. obs: 36621 / % possible obs: 99.2 % / Observed criterion σ(I): 5 / Redundancy: 4.2 % / Rmerge(I) obs: 0.048 / Χ2: 1.072 / Net I/σ(I): 13.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3i7c Resolution: 1.88→43.22 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 6.153 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.9 Å2 / Biso mean: 37.7362 Å2 / Biso min: 16.64 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→43.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.88→1.928 Å / Total num. of bins used: 20
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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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