[English] 日本語
Yorodumi- PDB-3ma6: Crystal structure of kinase domain of TgCDPK1 in presence of 3BrB-PP1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ma6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of kinase domain of TgCDPK1 in presence of 3BrB-PP1 | ||||||
Components | Calmodulin-domain protein kinase 1 | ||||||
Keywords | TRANSFERASE / CDPK / parasitology / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information calcium-dependent protein serine/threonine kinase activity / 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: 2.5 Å | ||||||
Authors | Wernimont, A.K. / Qiu, W. / Amani, M. / Artz, J.D. / Hassani, A.A. / Senisterra, G. / Vedadi, M. / Sibley, L.D. / Lourido, S. / Shokat, K. ...Wernimont, A.K. / Qiu, W. / Amani, M. / Artz, J.D. / Hassani, A.A. / Senisterra, G. / Vedadi, M. / Sibley, L.D. / Lourido, S. / Shokat, K. / Zhang, C. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Hui, R. / Lin, Y.H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of kinase domain of TgCDPK1 in presence of 3BrB-PP1 Authors: Wernimont, A.K. / Qiu, W. / Amani, M. / Artz, J.D. / Hassani, A.A. / Senisterra, G. / Vedadi, M. / Sibley, L.D. / Lourido, S. / Shokat, K. / Zhang, C. / Arrowsmith, C.H. / Edwards, A.M. / ...Authors: Wernimont, A.K. / Qiu, W. / Amani, M. / Artz, J.D. / Hassani, A.A. / Senisterra, G. / Vedadi, M. / Sibley, L.D. / Lourido, S. / Shokat, K. / Zhang, C. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Hui, R. / Lin, Y.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ma6.cif.gz | 114.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ma6.ent.gz | 90.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ma6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/3ma6 ftp://data.pdbj.org/pub/pdb/validation_reports/ma/3ma6 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34574.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: CDPK1, TGME49_101440 / Plasmid: PET15MLH / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BJF5 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.92 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 3350, 0.2 M Ammonium Formate, 15% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97948 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 15, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97948 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 25619 / Num. obs: 25594 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 63.2 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.052 / Χ2: 1.812 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.895 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1272 / Rsym value: 0.626 / Χ2: 2.328 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Rfactor: 54.82 / Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→34.74 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.894 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 189.01 Å2 / Biso mean: 71.798 Å2 / Biso min: 23.73 Å2
| ||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.534 Å | ||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→34.74 Å
| ||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.6 Å / Total num. of bins used: 13
|