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Open data
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Basic information
Entry | Database: PDB / ID: 5t0r | ||||||
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Title | Synaptotagmin 1 C2A domain, cadmium-bound | ||||||
![]() | Synaptotagmin-1![]() | ||||||
![]() | METAL BINDING PROTEIN | ||||||
Function / homology | ![]() GABA synthesis, release, reuptake and degradation / Serotonin Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Taylor, A.B. / Hart, P.J. / Igumenova, T.I. | ||||||
![]() | ![]() Title: Non-Native Metal Ion Reveals the Role of Electrostatics in Synaptotagmin 1-Membrane Interactions. Authors: Katti, S. / Nyenhuis, S.B. / Her, B. / Srivastava, A.K. / Taylor, A.B. / Hart, P.J. / Cafiso, D.S. / Igumenova, T.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 43.6 KB | Display | ![]() |
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PDB format | ![]() | 28 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5t0sC ![]() 3f00S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | ![]() Mass: 14525.588 Da / Num. of mol.: 1 / Fragment: C2A domain residues 140-265 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CD / |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.15 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.01 M tri-sodium citrate, 16% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Dec 4, 2014 |
Radiation | Monochromator: Confocal Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.95→38.07 Å / Num. obs: 10075 / % possible obs: 96.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 24.19 Å2 / Rsym value: 0.107 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.2 / % possible all: 85 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3F00 Resolution: 1.95→38.07 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 22.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→38.07 Å
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Refine LS restraints |
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LS refinement shell |
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