[English] 日本語
Yorodumi- PDB-3ncg: Activated Calcium-Dependent Protein Kinase 1 from Cryptosporidium... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ncg | ||||||
---|---|---|---|---|---|---|---|
Title | Activated Calcium-Dependent Protein Kinase 1 from Cryptosporidium parvum (CpCDPK1) in complex with bumped kinase inhibitor NM-PP1 | ||||||
Components | Calmodulin-domain protein kinase 1 | ||||||
Keywords | 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 | Function and homology information 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 | Cryptosporidium parvum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.49 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ncg.cif.gz | 192.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ncg.ent.gz | 151.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ncg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ncg_validation.pdf.gz | 766.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ncg_full_validation.pdf.gz | 771.7 KB | Display | |
Data in XML | 3ncg_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 3ncg_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/3ncg ftp://data.pdbj.org/pub/pdb/validation_reports/nc/3ncg | HTTPS FTP |
-Related structure data
Related structure data | 3mwuSC 3n51C 3igoS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Gene: CDPK1, cgd3_920 / Plasmid: PET15MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A3FQ16, Ca2+/calmodulin-dependent protein kinase | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-BK1 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.09 % |
---|---|
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 |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.49→33.58 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.49→2.552 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|