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Open data
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Basic information
Entry | Database: PDB / ID: 8sw8 | ||||||
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Title | Crystal Structure of HaloTag7 bound to JF669-HaloTag ligand | ||||||
![]() | Haloalkane dehalogenase | ||||||
![]() | HYDROLASE / HaloTag / Self-Labeling Protein / Fluorescent Dye | ||||||
Function / homology | ![]() haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Farrants, H. / Schreiter, E.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A modular chemigenetic calcium indicator for multiplexed in vivo functional imaging Authors: Farrants, H. / Schreiter, E.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.9 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 665.6 KB | Display | ![]() |
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Full document | ![]() | 666.1 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 20.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34530.367 Da / Num. of mol.: 1 / Mutation: HaloTag7 engineered mutations Source method: isolated from a genetically manipulated source Details: Bound to synthetic fluorescent dye JF669-HaloTag ligand Source: (gene. exp.) ![]() Gene: dhaA / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-XSR / Mass: 722.888 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H47F3N3O5Si / Feature type: SUBJECT OF INVESTIGATION |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.22 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M ammonium phosphate monobasic, 0.1 M TRIS pH 8.5, 50% v/v (+/-)-2-methyl-2,4-pentanediol Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 22, 2020 |
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0006 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→58.647 Å / Num. obs: 26532 / % possible obs: 99.6 % / Redundancy: 26.3 % / CC1/2: 0.988 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.9→1.94 Å / Num. unique obs: 1637 / CC1/2: 0.904 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.595 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→58.647 Å
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Refine LS restraints |
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LS refinement shell |
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