+Open data
-Basic information
Entry | Database: PDB / ID: 3igo | ||||||
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Title | Crystal structure of Cryptosporidium parvum CDPK1, cgd3_920 | ||||||
Components | Calmodulin-domain protein kinase 1 | ||||||
Keywords | TRANSFERASE / parasite / kinase / cdpk / Structural Genomics / Structural Genomics Consortium / SGC / ATP-binding / Nucleotide-binding / Serine/threonine-protein kinase | ||||||
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 | Cryptosporidium parvum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Wernimont, A.K. / Artz, J.D. / Finnerty, P. / Amani, M. / Allali-Hassanali, A. / Vedadi, M. / Tempel, W. / MacKenzie, F. / Edwards, A.M. / Arrowsmith, C.H. ...Wernimont, A.K. / Artz, J.D. / Finnerty, P. / Amani, M. / Allali-Hassanali, A. / Vedadi, M. / Tempel, W. / MacKenzie, F. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Hui, R. / Lin, Y.H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Structures of apicomplexan calcium-dependent protein kinases reveal mechanism of activation by calcium. Authors: Wernimont, A.K. / Artz, J.D. / Finerty, P. / Lin, Y.H. / Amani, M. / Allali-Hassani, A. / Senisterra, G. / Vedadi, M. / Tempel, W. / Mackenzie, F. / Chau, I. / Lourido, S. / Sibley, L.D. / Hui, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3igo.cif.gz | 112.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3igo.ent.gz | 83 KB | Display | PDB format |
PDBx/mmJSON format | 3igo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3igo_validation.pdf.gz | 843.6 KB | Display | wwPDB validaton report |
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Full document | 3igo_full_validation.pdf.gz | 854.4 KB | Display | |
Data in XML | 3igo_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 3igo_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/3igo ftp://data.pdbj.org/pub/pdb/validation_reports/ig/3igo | HTTPS FTP |
-Related structure data
Related structure data | 3hx4C 3hztC 3ku2C 3dxnS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 56152.793 Da / Num. of mol.: 1 / Fragment: UNP residues 70-538 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Gene: cgd3_920 / Plasmid: pET15MHL / Production host: Escherichia coli (E. coli) / References: UniProt: A3FQ16 |
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-Non-polymers , 6 types, 140 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ANP / | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-SRT / | #6: Chemical | ChemComp-PO4 / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3350, 0.2 M Diammonium tartrate, 2 mM ANP, CaCl2, TCEP, 4 mM MgCl2, 30% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 25110 / Num. obs: 25110 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.053 / Χ2: 1.262 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 1.65 / Num. unique all: 2502 / Rsym value: 0.741 / Χ2: 1.29 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3DXN Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.187 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.802 / SU B: 15.855 / SU ML: 0.186 / SU R Cruickshank DPI: 0.303 / SU Rfree: 0.234 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY.
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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: 112.62 Å2 / Biso mean: 29.329 Å2 / Biso min: 11.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.31 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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