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Yorodumi- PDB-3t3u: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t3u | ||||||
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Title | Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with Bumped Kinase Inhibitor, RM-1-130 | ||||||
Components | Calmodulin-domain protein kinase 1 | ||||||
Keywords | transferase/transferase inhibitor / serine/threonine protein kinase / transferase / calcium-binding / ATP-binding / calmodulin / EF hand / bumped kinase inhibitor / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information protein serine/threonine kinase activity / calcium ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å | ||||||
Authors | Larson, E.T. / Merritt, E.A. | ||||||
Citation | 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. #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. #2: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t3u.cif.gz | 201.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t3u.ent.gz | 160.5 KB | Display | PDB format |
PDBx/mmJSON format | 3t3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t3u_validation.pdf.gz | 732.5 KB | Display | wwPDB validaton report |
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Full document | 3t3u_full_validation.pdf.gz | 737 KB | Display | |
Data in XML | 3t3u_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 3t3u_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/3t3u ftp://data.pdbj.org/pub/pdb/validation_reports/t3/3t3u | HTTPS FTP |
-Related structure data
Related structure data | 3sx9C 3sxfC 3t3vC 3upxC 3upzC 3uqfC 3uqgC 3v51C 3v5pC 3v5tC 3i7bS S: Starting model for refinement C: citing same article (ref.) |
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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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Details | biological unit is the same as AU |
-Components
#1: Protein | Mass: 55226.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: residues 1-29 were replaced with a cleavable His-tag plus linker during cloning; tag was cleaved prior to crystallization Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: AAG53993, CDPK1, TGGT1_059880, TGVEG_042030 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9BJF5, Ca2+/calmodulin-dependent protein kinase | ||
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#2: Chemical | ChemComp-BK6 / | ||
#3: Chemical | ChemComp-DMS / | ||
#4: Chemical | #5: 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: 2.05 Å3/Da / Density % sol: 39.86 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 24% PEG 3350, 0.275 M ammonium citrate, 5 mM DTT, 2.3 mM RM-1-130; mother liquor supplemented with 15% ethylene glycol prior to freezing in LN2, pH 7.0, vapor diffusion, sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 8, 2010 |
Diffraction measurement | Details: 1.00 degrees, 8.2 sec, detector distance 300.00 mm |
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: 0.97945 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.095 / Number: 99477 |
Reflection | Resolution: 2.1→60 Å / Num. obs: 26082 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 14.401 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 1.457 / Rsym value: 0.887 / % possible all: 100 |
Cell measurement | Reflection used: 99477 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3i7b Resolution: 2.1→39.48 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.182 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 11.567 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.199 / 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: 114.33 Å2 / Biso mean: 42.208 Å2 / Biso min: 15.35 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→39.48 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / 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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