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Open data
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Basic information
Entry | Database: PDB / ID: 4mx9 | ||||||
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Title | CDPK1 from Neospora caninum in complex with inhibitor UW1294 | ||||||
![]() | Calmodulin-like domain protein kinase isoenzyme gamma, related | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / serine/threonine protein kinase / transferase / calcium-binding / ATP-binding / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Merritt, E.A. | ||||||
![]() | ![]() Title: Neospora caninum Calcium-Dependent Protein Kinase 1 Is an Effective Drug Target for Neosporosis Therapy. Authors: Ojo, K.K. / Reid, M.C. / Kallur Siddaramaiah, L. / Muller, J. / Winzer, P. / Zhang, Z. / Keyloun, K.R. / Vidadala, R.S. / Merritt, E.A. / Hol, W.G. / Maly, D.J. / Fan, E. / Van Voorhis, W.C. / Hemphill, A. #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 | ![]() | 202 KB | Display | ![]() |
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PDB format | ![]() | 162.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4m97SC ![]() 4mxaC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | biological unit is the same as AU |
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Components
#1: Protein | Mass: 55083.688 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-506 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: F0V9W9, Ca2+/calmodulin-dependent protein kinase |
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#2: Chemical | ChemComp-2E8 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: protein solution: 25 mM HEPES pH 7.0, 0.5 M NaCl, 5% glycerol, 5 mM DTT, 20 mM EGTA, 3mg/ml protein, 0.2 mM UW1294, 1% DMSO; crystallization buffer: 30% PEG 3350, 0.2 M ammonium citrate, 0.1 ...Details: protein solution: 25 mM HEPES pH 7.0, 0.5 M NaCl, 5% glycerol, 5 mM DTT, 20 mM EGTA, 3mg/ml protein, 0.2 mM UW1294, 1% DMSO; crystallization buffer: 30% PEG 3350, 0.2 M ammonium citrate, 0.1 M BisTris pH 5.3, 5 mM DTT, vapor diffusion, sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2013 | |||||||||||||||
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97939 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 3.1→65.3 Å / Num. obs: 7664 / % possible obs: 91.7 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.264 / Net I/σ(I): 4.5 | |||||||||||||||
Reflection shell | Rmerge(I) obs: 0.011 / Diffraction-ID: 1 / Redundancy: 2.6 %
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4M97 Resolution: 3.1→48.76 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.845 / WRfactor Rfree: 0.2885 / WRfactor Rwork: 0.2485 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7611 / SU B: 67.99 / SU ML: 0.541 / SU R Cruickshank DPI: 0.6214 / SU Rfree: 0.6739 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.674 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 209.04 Å2 / Biso mean: 78.5996 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→48.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.18 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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