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Yorodumi- PDB-4ov2: Crystal structure of C-terminally truncated Neuronal Calcium Sens... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ov2 | ||||||
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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 | CALCIUM BINDING PROTEIN | ||||||
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: 2.6 Å | ||||||
Authors | Pandaleneni, S. / Burgoyne, R. / Mayans, O. / Lian, L.-Y. | ||||||
Citation | Journal: To be Published Title: Crystal structure of C-terminally truncated Neuronal Calcium Sensor (NCS-1) from Rattus norvegicus Authors: Pandaleneni, S. / Burgoyne, R. / Mayans, O. / 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 | 4ov2.cif.gz | 275.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ov2.ent.gz | 222.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ov2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/4ov2 ftp://data.pdbj.org/pub/pdb/validation_reports/ov/4ov2 | HTTPS FTP |
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-Related structure data
Related structure data | 2you S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 20671.223 Da / Num. of mol.: 4 / Fragment: C-terminal truncation (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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.39 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6 Details: 0.2 M sodium chloride, 0.1 M MES, pH 6.0, 16% w/v PEG6000, VAPOR DIFFUSION, SITTING DROP |
-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: 2.6→66.594 Å / Num. obs: 20185 / % possible obs: 98.8 % / Redundancy: 3 % / Rsym value: 0.2 / Net I/σ(I): 2.3 |
Reflection shell | Resolution: 2.6→2.77 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.1 / Rsym value: 0.619 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YOU 2you Resolution: 2.6→66.594 Å / SU ML: 0.52 / σ(F): 1.37 / Phase error: 38.6 / 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: 2.6→66.594 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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