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- PDB-7ziw: X-ray structure of the haloalkane dehalogenase HaloTag7 bound to ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ziw | ||||||
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Title | X-ray structure of the haloalkane dehalogenase HaloTag7 bound to a butyltrifluoromethanesulfonamide tetramethylrhodamine ligand (TMR-T4) | ||||||
![]() | Haloalkane dehalogenase | ||||||
![]() | HYDROLASE / haloalkane dehalogenase / HaloTag / HaloTag7 / Self-Labeling Protein / Fluorophore / Tetramethylrhodamine | ||||||
Function / homology | ![]() haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tarnawski, M. / Kompa, J. / Johnsson, K. / Hiblot, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: X-ray structure of the haloalkane dehalogenase HaloTag7 bound to a butyltrifluoromethanesulfonamide tetramethylrhodamine ligand (FSAm(4)-TMR) Authors: Tarnawski, M. / Kompa, J. / Johnsson, K. / Hiblot, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155.9 KB | Display | ![]() |
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PDB format | ![]() | 103.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 910.8 KB | Display | ![]() |
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Full document | ![]() | 934.9 KB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 34.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6y7aS S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33225.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #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: 2.27 Å3/Da / Density % sol: 45.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M MES pH 6.0, 1.0 M lithium chloride, 22% (m/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 16, 2020 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00007 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→50 Å / Num. obs: 30065 / % possible obs: 75.1 % / Redundancy: 2.06 % / Biso Wilson estimate: 10.09 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.093 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.99→2.07 Å / Redundancy: 2.18 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1504 / CC1/2: 0.844 / % possible all: 32.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6Y7A Resolution: 1.99→44.68 Å / SU ML: 0.2554 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.1827 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→44.68 Å
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Refine LS restraints |
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LS refinement shell |
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