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- PDB-8p6g: Crystal structure of the improved version of the Genetically Enco... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8p6g | ||||||
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Title | Crystal structure of the improved version of the Genetically Encoded Green Calcium Indicator YTnC2-5 | ||||||
![]() | Genetically Encoded Green Calcium Indicator YTnC2-5 based on Troponin C from toadfish | ||||||
![]() | FLUORESCENT PROTEIN / calcium sensor / indicator / TNC / troponin / GECI / YTnC2 | ||||||
Function / homology | DI(HYDROXYETHYL)ETHER![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Boyko, K.M. / Nikolaeva, A.Y. / Subach, O.M. / Vlaskina, A.V. / Agapova, Y.K. / Popov, V.O. / Subach, F.V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: YTnC2, an improved genetically encoded green calcium indicator based on toadfish troponin C. Authors: Subach, O.M. / Vlaskina, A.V. / Agapova, Y.K. / Nikolaeva, A.Y. / Varizhuk, A.M. / Podgorny, O.V. / Piatkevich, K.D. / Patrushev, M.V. / Boyko, K.M. / Subach, F.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 208 KB | Display | ![]() |
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PDB format | ![]() | 165.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.5 KB | Display | ![]() |
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Full document | ![]() | 458.1 KB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 31.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 35822.918 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.18 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 0.2M Sodium fluoride, 0.1M Bis-tris propane, 20% PEG 3350 pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→46.14 Å / Num. obs: 55880 / % possible obs: 100 % / Redundancy: 20.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.313 / Rpim(I) all: 0.071 / Rrim(I) all: 0.321 / Χ2: 1.02 / Net I/σ(I): 6.5 / Num. measured all: 1130475 |
Reflection shell | Resolution: 1.95→2 Å / % possible obs: 100 % / Redundancy: 19.1 % / Rmerge(I) obs: 3.567 / Num. measured all: 76035 / Num. unique obs: 3979 / CC1/2: 0.468 / Rpim(I) all: 0.83 / Rrim(I) all: 3.663 / Χ2: 1.04 / Net I/σ(I) obs: 0.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.401 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→46.14 Å
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Refine LS restraints |
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