+Open data
-Basic information
Entry | Database: PDB / ID: 5iri | ||||||
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Title | Structure of the mouse SAD-B AIS-KA1 fragment | ||||||
Components | Serine/threonine-protein kinase BRSK1 | ||||||
Keywords | TRANSFERASE / auto-inhibition / kinase associate-1 domain | ||||||
Function / homology | Function and homology information synaptic vesicle cycle / distal axon / microtubule cytoskeleton organization involved in establishment of planar polarity / protein serine/threonine kinase activity => GO:0004674 / neurotransmitter secretion / tau-protein kinase / gamma-tubulin binding / regulation of neuron projection development / regulation of axonogenesis / establishment of cell polarity ...synaptic vesicle cycle / distal axon / microtubule cytoskeleton organization involved in establishment of planar polarity / protein serine/threonine kinase activity => GO:0004674 / neurotransmitter secretion / tau-protein kinase / gamma-tubulin binding / regulation of neuron projection development / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity / presynaptic active zone / mitotic G2 DNA damage checkpoint signaling / associative learning / centrosome duplication / cellular response to glucose starvation / response to UV / axonogenesis / neuron projection morphogenesis / regulation of synaptic plasticity / neuron differentiation / G2/M transition of mitotic cell cycle / synaptic vesicle / cell junction / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA damage response / protein kinase binding / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Ma, H. / Wu, J.X. / Wang, J. / Wu, J.W. | ||||||
Citation | Journal: Biosci.Biotechnol.Biochem. / Year: 2016 Title: Structure and inhibition analysis of the mouse SAD-B C-terminal fragment Authors: Ma, H. / Wu, J.X. / Wang, J. / Wang, Z.X. / Wu, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iri.cif.gz | 54.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iri.ent.gz | 37.9 KB | Display | PDB format |
PDBx/mmJSON format | 5iri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/5iri ftp://data.pdbj.org/pub/pdb/validation_reports/ir/5iri | HTTPS FTP |
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-Related structure data
Related structure data | 4yomS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15348.308 Da / Num. of mol.: 2 / Fragment: UNP residues 592-719 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Brsk1, Gm1100, Sadb / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(ED3) / References: UniProt: Q5RJI5, tau-protein kinase #2: 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: 2.81 Å3/Da / Density % sol: 56.25 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.51 / Details: 0.1 M HEPES, 3M KCl, 0.01 M Urea |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2015 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 9101 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 53.7 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 23.84 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 5.36 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YOM Resolution: 2.8→26.3 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.7 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→26.3 Å
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Refine LS restraints |
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LS refinement shell |
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