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- PDB-6zsm: Crystal structure of rsGCaMP double mutant Ile80His/Val116Ile in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zsm | ||||||
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Title | Crystal structure of rsGCaMP double mutant Ile80His/Val116Ile in the ON state (non-illuminated) | ||||||
![]() | Green fluorescent protein,Green fluorescent protein,Calmodulin | ||||||
![]() | FLUORESCENT PROTEIN / reversible switchable fluorescent protein / calcium sensor / calmodulin | ||||||
Function / homology | ![]() enzyme regulator activity / bioluminescence / generation of precursor metabolites and energy / calcium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Janowski, R. / Fuenzalida-Werner, J.P. / Mishra, K. / Stiel, A.C. / Niessing, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Genetically encoded photo-switchable molecular sensors for optoacoustic and super-resolution imaging. Authors: Mishra, K. / Fuenzalida-Werner, J.P. / Pennacchietti, F. / Janowski, R. / Chmyrov, A. / Huang, Y. / Zakian, C. / Klemm, U. / Testa, I. / Niessing, D. / Ntziachristos, V. / Stiel, A.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189.6 KB | Display | ![]() |
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PDB format | ![]() | 146.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.3 KB | Display | ![]() |
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Full document | ![]() | 476.3 KB | Display | |
Data in XML | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 35.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tv7C ![]() 6ya9SC ![]() 6zsnC ![]() 7augC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 47324.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: GFP / Production host: ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.49 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 0.20 M sodium formate, 0.1 M Bis-Tris-Propane buffer pH 8.5, 19% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 25, 2020 |
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→47.46 Å / Num. obs: 53375 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 41 Å2 / CC1/2: 1 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3888 / CC1/2: 0.674 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ya9 Resolution: 1.95→47.46 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.228 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 920.26 Å2 / Biso mean: 37.825 Å2 / Biso min: 21.09 Å2
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Refinement step | Cycle: final / Resolution: 1.95→47.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 2.9928 Å / Origin y: 40.3849 Å / Origin z: 22.504 Å
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