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- PDB-3ncg: Activated Calcium-Dependent Protein Kinase 1 from Cryptosporidium... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ncg | ||||||
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Title | Activated Calcium-Dependent Protein Kinase 1 from Cryptosporidium parvum (CpCDPK1) in complex with bumped kinase inhibitor NM-PP1 | ||||||
![]() | Calmodulin-domain protein kinase 1 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / serine/threonine protein kinase / transferase / calcium-binding / ATP-binding / calmodulin / bumped kinase inhibitor / transferase-transferase inhibitor complex / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP | ||||||
Function / homology | ![]() calcium-dependent protein serine/threonine kinase activity / calcium/calmodulin-dependent protein kinase activity / calmodulin binding / intracellular signal transduction / calcium ion binding / ATP binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Larson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP) | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 192.1 KB | Display | ![]() |
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PDB format | ![]() | 151.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3mwuSC ![]() 3n51C ![]() 3igoS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 56152.793 Da / Num. of mol.: 1 / Fragment: CpCDPK1, residues 70-538 Source method: isolated from a genetically manipulated source Details: residues 1-69 were replaced with a His-tag and linker during cloning Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A3FQ16, Ca2+/calmodulin-dependent protein kinase | ||||
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#2: Chemical | #3: Chemical | ChemComp-BK1 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 32% PEG 3350, 0.35 M di-ammonium tartrate (not pH'ed), 5 mM TCEP, 3 mM MgCl2, 1 mM CaCl2, 2 mM inhibitor, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→35 Å / Num. obs: 17762 / % possible obs: 95.3 % / Observed criterion σ(I): 5 / Redundancy: 3.7 % / Biso Wilson estimate: 52.9 Å2 / Rmerge(I) obs: 0.092 / Χ2: 1.028 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.49→2.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1775 / Χ2: 1.065 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3mwu, 3igo Resolution: 2.49→33.58 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.867 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 22.201 / SU ML: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.36 / 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: 147.36 Å2 / Biso mean: 58.73 Å2 / Biso min: 20.65 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→33.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.49→2.552 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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