+Open data
-Basic information
Entry | Database: PDB / ID: 3c0h | ||||||
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Title | CASK CaM-Kinase Domain- AMPPNP complex, P1 form | ||||||
Components | Peripheral plasma membrane protein CASK | ||||||
Keywords | TRANSFERASE / CASK / neurexin / Ca2+/calmodulin dependent protein kinase / Mg2+ / synaptic plasticity / pseudokinase / MAGUK / membrane-associated guanylate kinase / ATP-binding / Calmodulin-binding / Magnesium / Metal-binding / Nucleotide-binding / Nucleus / Serine/threonine-protein kinase / SH3 domain | ||||||
Function / homology | Function and homology information negative regulation of cellular response to growth factor stimulus / guanylate kinase activity / Dopamine Neurotransmitter Release Cycle / neurexin family protein binding / regulation of neurotransmitter secretion / negative regulation of wound healing / nuclear lamina / calcium ion import / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins ...negative regulation of cellular response to growth factor stimulus / guanylate kinase activity / Dopamine Neurotransmitter Release Cycle / neurexin family protein binding / regulation of neurotransmitter secretion / negative regulation of wound healing / nuclear lamina / calcium ion import / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / Nephrin family interactions / ciliary membrane / regulation of synaptic vesicle exocytosis / Syndecan interactions / negative regulation of cell-matrix adhesion / positive regulation of calcium ion import / basement membrane / negative regulation of keratinocyte proliferation / establishment of localization in cell / Schaffer collateral - CA1 synapse / nuclear matrix / cell-cell junction / actin cytoskeleton / presynaptic membrane / basolateral plasma membrane / vesicle / calmodulin binding / non-specific serine/threonine protein kinase / cell adhesion / phosphorylation / signaling receptor binding / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / positive regulation of transcription by RNA polymerase II / ATP binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Wahl, M.C. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2008 Title: CASK Functions as a Mg2+-independent neurexin kinase Authors: Mukherjee, K. / Sharma, M. / Urlaub, H. / Bourenkov, G.P. / Jahn, R. / Sudhof, T.C. / Wahl, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c0h.cif.gz | 139.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c0h.ent.gz | 107.1 KB | Display | PDB format |
PDBx/mmJSON format | 3c0h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/3c0h ftp://data.pdbj.org/pub/pdb/validation_reports/c0/3c0h | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 5 - 304 / Label seq-ID: 19 - 318
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-Components
#1: Protein | Mass: 39257.121 Da / Num. of mol.: 2 / Fragment: CaM-Kinase Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASK / Plasmid: pGEX-6T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: O14936, non-specific serine/threonine protein kinase #2: Chemical | #3: 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: 2.45 Å3/Da / Density % sol: 49.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 12.5%(v/v) ethylene glycol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 29, 2004 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 30806 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Biso Wilson estimate: 64.2 Å2 / Rsym value: 0.108 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 3312 / Rsym value: 0.717 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: rat CamKI Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 15.395 / SU ML: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.373 / ESU R Free: 0.246 / 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: 51.677 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2399 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.359 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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