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Yorodumi- PDB-7zj0: X-ray structure of the haloalkane dehalogenase HaloTag7 bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zj0 | ||||||
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Title | X-ray structure of the haloalkane dehalogenase HaloTag7 bound to a pentylmethanesulfonamide tetramethylrhodamine ligand (TMR-S5) | ||||||
Components | Haloalkane dehalogenase | ||||||
Keywords | HYDROLASE / haloalkane dehalogenase / HaloTag / HaloTag7 / Self-Labeling Protein / Fluorophore / Tetramethylrhodamine | ||||||
Function / homology | Function and homology information haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance Similarity search - Function | ||||||
Biological species | Rhodococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Tarnawski, M. / Kompa, J. / Johnsson, K. / Hiblot, J. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2023 Title: Exchangeable HaloTag Ligands for Super-Resolution Fluorescence Microscopy. Authors: Kompa, J. / Bruins, J. / Glogger, M. / Wilhelm, J. / Frei, M.S. / Tarnawski, M. / D'Este, E. / Heilemann, M. / Hiblot, J. / Johnsson, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zj0.cif.gz | 173.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zj0.ent.gz | 109.9 KB | Display | PDB format |
PDBx/mmJSON format | 7zj0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/7zj0 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/7zj0 | HTTPS FTP |
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-Related structure data
Related structure data | 7ziyC 7zizC 6y7aS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Rhodococcus sp. (bacteria) / Gene: dhaA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3G3, haloalkane dehalogenase #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.94 % |
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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, 20% (m/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999884 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 30, 2020 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999884 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 85890 / % possible obs: 91.4 % / Redundancy: 1.93 % / Biso Wilson estimate: 16.69 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.039 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.5→1.6 Å / Redundancy: 1.99 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.51 / Num. unique obs: 14710 / CC1/2: 0.77 / % possible all: 88.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Y7A Resolution: 1.5→43.36 Å / SU ML: 0.1916 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.5251 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: 19.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→43.36 Å
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Refine LS restraints |
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LS refinement shell |
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