+Open data
-Basic information
Entry | Database: PDB / ID: 4o38 | |||||||||
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Title | Crystal structure of the human cyclin G associated kinase (GAK) | |||||||||
Components | Cyclin-G-associated kinaseGAK (protein) | |||||||||
Keywords | TRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / protein kinase / serine/threonine kinase / cyclin G / p53 / clathrine / membrane trafficking / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / ATP-binding / Cell cycle / Cell junction / Golgi apparatus / Kinase / Nucleotide-binding / Phosphoprotein | |||||||||
Function / homology | Function and homology information regulation of clathrin coat assembly / synaptic vesicle uncoating / Golgi to lysosome transport / protein localization to Golgi apparatus / clathrin coat assembly / clathrin coat disassembly / clathrin-dependent endocytosis / endoplasmic reticulum organization / clathrin-coated vesicle / clathrin binding ...regulation of clathrin coat assembly / synaptic vesicle uncoating / Golgi to lysosome transport / protein localization to Golgi apparatus / clathrin coat assembly / clathrin coat disassembly / clathrin-dependent endocytosis / endoplasmic reticulum organization / clathrin-coated vesicle / clathrin binding / Golgi Associated Vesicle Biogenesis / Golgi organization / chaperone cofactor-dependent protein refolding / intracellular transport / receptor-mediated endocytosis / cyclin binding / protein localization to plasma membrane / negative regulation of neuron projection development / presynapse / Clathrin-mediated endocytosis / protein-folding chaperone binding / vesicle / non-specific serine/threonine protein kinase / cell cycle / phosphorylation / focal adhesion / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / perinuclear region of cytoplasm / Golgi apparatus / ATP binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.097 Å | |||||||||
Authors | Zhang, R. / Hatzos-Skintges, C. / Weger, A. / Chaikuad, A. / Eswaran, J. / Fedorov, O. / King, O. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. ...Zhang, R. / Hatzos-Skintges, C. / Weger, A. / Chaikuad, A. / Eswaran, J. / Fedorov, O. / King, O. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structural Genomics Consortium (SGC) | |||||||||
Citation | Journal: To be Published Title: Crystal structure of the human cyclin G associated kinase (GAK) Authors: Zhang, R. / Hatzos-Skintges, C. / Weger, A. / Chaikuad, A. / Eswaran, J. / Fedorov, O. / King, O. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S. / Joachimiak, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o38.cif.gz | 232.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o38.ent.gz | 196.9 KB | Display | PDB format |
PDBx/mmJSON format | 4o38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/4o38 ftp://data.pdbj.org/pub/pdb/validation_reports/o3/4o38 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Details | The dimeric form in the asymmetric unit could occur at high concentration, and represent an inactive form of the kinase. Monomeric state is the active form. |
-Components
#1: Protein | Mass: 38202.582 Da / Num. of mol.: 2 / Fragment: kinase domain (11-347) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GAK / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: O14976, non-specific serine/threonine protein kinase #2: Chemical | #3: Chemical | #4: 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: 2.67 Å3/Da / Density % sol: 53.87 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.0M succinic acid, 0.1M Bis-Tris Propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794, 0.97912 | |||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2009 / Details: mirrors | |||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.097→74.11 Å / Num. all: 48311 / Num. obs: 48245 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 36.6 | |||||||||
Reflection shell | Resolution: 2.097→2.14 Å / Redundancy: 14 % / Rmerge(I) obs: 0.957 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2356 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.097→74.11 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.986 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.144 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 55.877 Å2
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Refine analyze | Luzzati coordinate error obs: 0.265 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.097→74.11 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 15976 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.097→2.151 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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