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Yorodumi- PDB-2cmw: Structure of Human Casein kinase 1 gamma-1 in complex with 2-(2- ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cmw | ||||||
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Title | Structure of Human Casein kinase 1 gamma-1 in complex with 2-(2- Hydroxyethylamino)-6-(3-chloroanilino)-9-isopropylpurine | ||||||
Components | CASEIN KINASE I ISOFORM GAMMA-1 | ||||||
Keywords | TRANSFERASE / WNT SIGNALING PATHWAY / SERINE/THREONINE-PROTEIN KINASE / KINASE / ATP-BINDING / PHOSPHORYLATION / NUCLEOTIDE-BINDING / SERINE/THREONINE PROTEIN KINASE | ||||||
Function / homology | Function and homology information Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Bunkoczi, G. / Rellos, P. / Das, S. / Savitsky, P. / Niesen, F. / Sobott, F. / Fedorov, O. / Pike, A.C.W. / von Delft, F. / Sundstrom, M. ...Bunkoczi, G. / Rellos, P. / Das, S. / Savitsky, P. / Niesen, F. / Sobott, F. / Fedorov, O. / Pike, A.C.W. / von Delft, F. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Knapp, S. | ||||||
Citation | Journal: To be Published Title: Structure of Human Casein Kinase 1 Gamma-1 in Complex with 2-(2-Hydroxyethylamino)-6-(3-Chloroanilino)-9-Isopropylpurine (Casp Target) Authors: Bunkoczi, G. / Rellos, P. / Das, S. / Savitsky, P. / Niesen, F. / Sobott, F. / Fedorov, O. / Pike, A.C.W. / von Delft, F. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cmw.cif.gz | 86 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cmw.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 2cmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/2cmw ftp://data.pdbj.org/pub/pdb/validation_reports/cm/2cmw | HTTPS FTP |
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-Related structure data
Related structure data | 2chlS 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
#1: Protein | Mass: 36142.574 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 45-352 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9HCP0, non-specific serine/threonine protein kinase | ||||||||||
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#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | Compound details | CASEIN KINASES ARE OPERATIONALLY DEFINED BY THEIR PREFERENTIAL UTILIZATION OF ACIDIC PROTEINS SUCH ...CASEIN KINASES ARE OPERATIONA | Sequence details | NTERMINAL SER-MET ARE DERIVED FROM CLONING | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52 % |
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Crystal grow | pH: 5.5 Details: 0.1M BIS-TRIS PH 5.5, 0.05M AMMONIUM ACETATE, 12% PEG 10K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9765 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 6, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 38266 / % possible obs: 99.7 % / Observed criterion σ(I): 3.6 / Redundancy: 7.83 % / Biso Wilson estimate: 23.56 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.76 |
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 6.72 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.62 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CHL Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.147 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DIETHYLAMINO TAIL OF LIGAND IS DISORDERED AND HAS NOT BEEN INCLUDED IN THE FINAL MODEL
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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 mean: 29.41 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→50 Å
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Refine LS restraints |
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