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Yorodumi- PDB-3i7b: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i7b | ||||||
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Title | Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with bumped kinase inhibitor NM-PP1 | ||||||
Components | Calmodulin-domain protein kinase 1 | ||||||
Keywords | TRANSFERASE / protein kinase / calmodulin / EF hand / bumped kinase inhibitor / ATP-binding / kinase / nucleotide-binding / serine/threonine-protein kinase / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP | ||||||
Function / homology | Function and homology information calcium-dependent protein serine/threonine kinase activity / calcium/calmodulin-dependent protein kinase activity / calmodulin binding / intracellular signal transduction / phosphorylation / calcium ion binding / ATP binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.988 Å | ||||||
Authors | Larson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP) | ||||||
Citation | 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. #1: 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.R. / Verlinde, C.L.M.J. / White Jr, A.C. / ...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.R. / Verlinde, C.L.M.J. / White Jr, A.C. / 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 | 3i7b.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i7b.ent.gz | 85.1 KB | Display | PDB format |
PDBx/mmJSON format | 3i7b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i7b_validation.pdf.gz | 826.6 KB | Display | wwPDB validaton report |
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Full document | 3i7b_full_validation.pdf.gz | 830.8 KB | Display | |
Data in XML | 3i7b_validation.xml.gz | 19 KB | Display | |
Data in CIF | 3i7b_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/3i7b ftp://data.pdbj.org/pub/pdb/validation_reports/i7/3i7b | HTTPS FTP |
-Related structure data
Related structure data | 3i79SC 3i7cC 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: 55226.914 Da / Num. of mol.: 1 / Fragment: residues 30-507 Source method: isolated from a genetically manipulated source Details: residues 1-29 were replaced with a 3C cleavable His-tag and linker during cloning; tag was cleaved prior to crystallization Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: CDPK1, TgCDPK1 / 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-BK1 / | ||||
#3: Chemical | #4: Chemical | ChemComp-DMS / | #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: 2.02 Å3/Da / Density % sol: 39.22 % |
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Crystal grow | Temperature: 298 K / Method: sitting drop vapor diffusion / pH: 6.5 Details: 26% PEG 3350, 0.18 M ammonium citrate, 4 mM NM-PP1; cryoprotected with 10% ethylene glycol, pH 6.5, sitting drop vapor diffusion, 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: May 20, 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: 1.988→50 Å / Num. obs: 30350 / % possible obs: 99.8 % / Observed criterion σ(I): 5 / Redundancy: 4.2 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.039 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.988→2.06 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2975 / Χ2: 1.07 / % possible all: 98.1 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 45.21 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3I79 Resolution: 1.988→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 9.825 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES ARE RESIDUAL ONLY
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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: 62.84 Å2 / Biso mean: 19.845 Å2 / Biso min: 3.93 Å2
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Refinement step | Cycle: LAST / Resolution: 1.988→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.988→2.04 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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