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Yorodumi- PDB-4y5q: Activated Calcium-Dependent Protein Kinase 1 from Cryptosporidium... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y5q | ||||||
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Title | Activated Calcium-Dependent Protein Kinase 1 from Cryptosporidium parvum (CpCDPK1) in complex with AMP | ||||||
Components | Calmodulin-domain protein kinase 1, putative | ||||||
Keywords | TRANSFERASE / serine/threonine protein kinase / calcium-binding / ATP-binding / calmodulin / bumped kinase inhibitor / 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 Iowa II (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Merritt, E.A. / Larson, E.T. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Activated Calcium-Dependent Protein Kinase 1 from Cryptosporidium parvum (CpCDPK1) in complex with AMP Authors: Merritt, E.A. / Larson, E.T. / Medical Structural Genomics of Pathogenic Protozoa #1: Journal: J. Med. Chem. / Year: 2012 Title: Multiple determinants for selective inhibition of apicomplexan calcium-dependent protein kinase CDPK1. Authors: Larson, E.T. / Ojo, K.K. / Murphy, R.C. / Johnson, S.M. / Zhang, Z. / Kim, J.E. / Leibly, D.J. / Fox, A.M. / Reid, M.C. / Dale, E.J. / Perera, B.G. / Kim, J. / Hewitt, S.N. / Hol, W.G. / ...Authors: Larson, E.T. / Ojo, K.K. / Murphy, R.C. / Johnson, S.M. / Zhang, Z. / Kim, J.E. / Leibly, D.J. / Fox, A.M. / Reid, M.C. / Dale, E.J. / Perera, B.G. / Kim, J. / Hewitt, S.N. / Hol, W.G. / Verlinde, C.L. / Fan, E. / Van Voorhis, W.C. / Maly, D.J. / Merritt, E.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y5q.cif.gz | 202.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y5q.ent.gz | 158.3 KB | Display | PDB format |
PDBx/mmJSON format | 4y5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4y5q_validation.pdf.gz | 805.3 KB | Display | wwPDB validaton report |
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Full document | 4y5q_full_validation.pdf.gz | 815.4 KB | Display | |
Data in XML | 4y5q_validation.xml.gz | 20 KB | Display | |
Data in CIF | 4y5q_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/4y5q ftp://data.pdbj.org/pub/pdb/validation_reports/y5/4y5q | HTTPS FTP |
-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 56152.793 Da / Num. of mol.: 1 / Fragment: 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 Iowa II (eukaryote) Gene: cgd3_920 / Plasmid: PET15MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3FQ16 | ||||
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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-AMP / | #4: Water | ChemComp-HOH / | |
-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: 47.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 27% PEG 3350, 0.27 M ammonium tartrate (pH 7.0), 6% PEG 400, 5 mM TCEP, 4 mM MgCl2, 2 mM CaCl2, 2 mM AMP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9797 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 4, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.994→40.272 Å / Num. all: 34688 / Num. obs: 34688 / % possible obs: 97 % / Redundancy: 3.8 % / Biso Wilson estimate: 31.5 Å2 / Rpim(I) all: 0.043 / Rrim(I) all: 0.085 / Rsym value: 0.064 / Net I/av σ(I): 8.124 / Net I/σ(I): 8.5 / Num. measured all: 132992 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→39.38 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2306 / WRfactor Rwork: 0.1815 / FOM work R set: 0.7992 / SU B: 10.703 / SU ML: 0.141 / SU R Cruickshank DPI: 0.1725 / SU Rfree: 0.1593 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.159 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 168.36 Å2 / Biso mean: 61.822 Å2 / Biso min: 31.37 Å2
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Refinement step | Cycle: final / Resolution: 2→39.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.995→2.047 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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