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Yorodumi- PDB-4yru: Crystal structure of C-terminally truncated Neuronal Calcium Sens... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yru | ||||||
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Title | Crystal structure of C-terminally truncated Neuronal Calcium Sensor (NCS-1) from Rattus norvegicus | ||||||
Components | Neuronal calcium sensor 1 | ||||||
Keywords | SIGNALING PROTEIN / EF-hand / Calcium sensor / C-terminal truncation | ||||||
Function / homology | Function and homology information calcium-dependent protein kinase inhibitor activity / calcium sensitive guanylate cyclase activator activity / regulation of presynaptic cytosolic calcium ion concentration / presynaptic cytosol / postsynaptic cytosol / regulation of neuron projection development / regulation of synaptic vesicle exocytosis / positive regulation of exocytosis / calyx of Held / voltage-gated calcium channel activity ...calcium-dependent protein kinase inhibitor activity / calcium sensitive guanylate cyclase activator activity / regulation of presynaptic cytosolic calcium ion concentration / presynaptic cytosol / postsynaptic cytosol / regulation of neuron projection development / regulation of synaptic vesicle exocytosis / positive regulation of exocytosis / calyx of Held / voltage-gated calcium channel activity / positive regulation of calcium-mediated signaling / postsynapse / postsynaptic density / axon / glutamatergic synapse / dendrite / calcium ion binding / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / magnesium ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Pandalaneni, S. / Karrupiah, V. / Mayans, O. / Derrick, J.P. / Lian, L.Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Neuronal Calcium Sensor-1 Binds the D2 Dopamine Receptor and G-protein-coupled Receptor Kinase 1 (GRK1) Peptides Using Different Modes of Interactions. Authors: Pandalaneni, S. / Karuppiah, V. / Saleem, M. / Haynes, L.P. / Burgoyne, R.D. / Mayans, O. / Derrick, J.P. / Lian, L.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yru.cif.gz | 272.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yru.ent.gz | 220.2 KB | Display | PDB format |
PDBx/mmJSON format | 4yru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/4yru ftp://data.pdbj.org/pub/pdb/validation_reports/yr/4yru | HTTPS FTP |
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-Related structure data
Related structure data | 5aeqC 5aerC 5afpC 2you 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20543.092 Da / Num. of mol.: 4 / Fragment: UNP residues 1-177 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ncs1, Flup, Freq / Production host: Escherichia coli (E. coli) / References: UniProt: P62168 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M MES pH6.0, 200mM NaCl,16% (w/v) PEG 6K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2013 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→66.59 Å / Num. obs: 16258 / % possible obs: 98 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 1.1 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3 % / Rmerge(I) obs: 0.374 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2you 2you Resolution: 2.8→66.59 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→66.59 Å
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Refine LS restraints |
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LS refinement shell |
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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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