+Open data
-Basic information
Entry | Database: PDB / ID: 3mfr | ||||||
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Title | CASK-4M CaM Kinase Domain, native | ||||||
Components | Peripheral plasma membrane protein CASK | ||||||
Keywords | TRANSFERASE / Catalytic mechanism / kinase catalysis / Mg2+-mediated phosphate transfer / protein kinase | ||||||
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 / Syndecan interactions / regulation of synaptic vesicle exocytosis / 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 / non-specific serine/threonine protein kinase / calmodulin binding / cell adhesion / phosphorylation / focal adhesion / protein serine kinase activity / signaling receptor binding / protein serine/threonine kinase activity / nucleolus / positive regulation of transcription by RNA polymerase II / ATP binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wahl, M.C. / Mukherjee, K. | ||||||
Citation | Journal: Sci.Signal. / Year: 2010 Title: Evolution of CASK into a Mg2+-sensitive kinase. Authors: Mukherjee, K. / Sharma, M. / Jahn, R. / Wahl, M.C. / Sudhof, T.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mfr.cif.gz | 82.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mfr.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 3mfr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mfr_validation.pdf.gz | 808.6 KB | Display | wwPDB validaton report |
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Full document | 3mfr_full_validation.pdf.gz | 814.6 KB | Display | |
Data in XML | 3mfr_validation.xml.gz | 16 KB | Display | |
Data in CIF | 3mfr_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/3mfr ftp://data.pdbj.org/pub/pdb/validation_reports/mf/3mfr | HTTPS FTP |
-Related structure data
Related structure data | 3mfsC 3mftC 3mfuC 3c0iS 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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-Components
#1: Protein | Mass: 39291.047 Da / Num. of mol.: 1 / Fragment: CASK-4M CaM kinase domain, residues 1-337 / Mutation: Pro22Ala, His145Glu, Gly162Asp, Cys146Asn Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASK, LIN2 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: O14936, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-ANP / |
#3: 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: 2.31 Å3/Da / Density % sol: 46.83 % |
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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: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. all: 27421 / Num. obs: 26982 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1269 / Rsym value: 0.684 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3C0I Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.318 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.184 / ESU R Free: 0.167 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.684 Å2
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Refine analyze | Luzzati coordinate error obs: 0.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 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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