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Yorodumi- PDB-3n51: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n51 | ||||||
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Title | Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with bumped kinase inhibitor RM-1-95 | ||||||
Components | Calmodulin-domain protein kinase 1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / serine/threonine protein kinase / transferase / calcium-binding / ATP-binding / calmodulin / bumped kinase inhibitor / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.1 Å | ||||||
Authors | Larson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP) | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2010 Title: Discovery of Potent and Selective Inhibitors of Calcium-Dependent Protein Kinase 1 (CDPK1) from C. parvum and T. gondii. Authors: Murphy, R.C. / Ojo, K.K. / Larson, E.T. / Castellanos-Gonzalez, A. / Perera, B.G. / Keyloun, K.R. / Kim, J.E. / Bhandari, J.G. / Muller, N.R. / Verlinde, C.L. / White, A.C. / Merritt, E.A. / ...Authors: Murphy, R.C. / Ojo, K.K. / Larson, E.T. / Castellanos-Gonzalez, A. / Perera, B.G. / Keyloun, K.R. / Kim, J.E. / Bhandari, J.G. / Muller, N.R. / Verlinde, C.L. / White, A.C. / Merritt, E.A. / Van Voorhis, W.C. / Maly, D.J. #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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n51.cif.gz | 200.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n51.ent.gz | 160 KB | Display | PDB format |
PDBx/mmJSON format | 3n51.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n51_validation.pdf.gz | 775.8 KB | Display | wwPDB validaton report |
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Full document | 3n51_full_validation.pdf.gz | 779 KB | Display | |
Data in XML | 3n51_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 3n51_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/3n51 ftp://data.pdbj.org/pub/pdb/validation_reports/n5/3n51 | HTTPS FTP |
-Related structure data
Related structure data | 3mwuC 3ncgC 3i7bS 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: 55226.914 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 and linker during cloning; 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-BK3 / |
#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-EDO / |
#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: 2.04 Å3/Da / Density % sol: 39.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 24% PEG 3350, 0.25 M ammonium citrate, 5 mM DTT, 2.3 mM RM-1-95; cryoprotected by quick dip into well soln + final conc. (4.5% SGPP buffer, 9% ethylene glycol, 2 mM RM-1-95), pH 6.5, VAPOR ...Details: 24% PEG 3350, 0.25 M ammonium citrate, 5 mM DTT, 2.3 mM RM-1-95; cryoprotected by quick dip into well soln + final conc. (4.5% SGPP buffer, 9% ethylene glycol, 2 mM RM-1-95), 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: BL7-1 / Wavelength: 0.976 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2009 |
Radiation | Monochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 26020 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 3.8 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.094 / Χ2: 1.002 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 1.1 / Num. unique all: 2590 / Χ2: 0.989 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3i7b Resolution: 2.1→39.45 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.186 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 11.388 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.203 / 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: 116.81 Å2 / Biso mean: 50.291 Å2 / Biso min: 21.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→39.45 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / 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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