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Yorodumi- PDB-8b6s: X-ray structure of the haloalkane dehalogenase HaloTag7 fusion to... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b6s | ||||||
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Title | X-ray structure of the haloalkane dehalogenase HaloTag7 fusion to the green fluorescent protein GFP (ChemoG1) labeled with a chloroalkane tetramethylrhodamine fluorophore substrate | ||||||
Components | Green fluorescent protein,Haloalkane dehalogenase | ||||||
Keywords | HYDROLASE / haloalkane dehalogenase / HaloTag / HaloTag7 / Self-Labeling Protein / green fluorescent protein / GFP / fluorophore / tetramethylerhodamine / TMR | ||||||
Function / homology | Function and homology information haloalkane dehalogenase / haloalkane dehalogenase activity / bioluminescence / generation of precursor metabolites and energy / response to toxic substance Similarity search - Function | ||||||
Biological species | Rhodococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Tarnawski, M. / Hellweg, L. / Hiblot, J. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2023 Title: A general method for the development of multicolor biosensors with large dynamic ranges. Authors: Hellweg, L. / Edenhofer, A. / Barck, L. / Huppertz, M.C. / Frei, M.S. / Tarnawski, M. / Bergner, A. / Koch, B. / Johnsson, K. / Hiblot, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b6s.cif.gz | 281.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b6s.ent.gz | 180.1 KB | Display | PDB format |
PDBx/mmJSON format | 8b6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/8b6s ftp://data.pdbj.org/pub/pdb/validation_reports/b6/8b6s | HTTPS FTP |
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-Related structure data
Related structure data | 8b6rC 8b6tC 1gflS 5y2xS 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: 59990.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Gene: GFP, dhaA / Production host: Escherichia coli (E. coli) References: UniProt: P42212, UniProt: P0A3G3, haloalkane dehalogenase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.19 Å3/Da / Density % sol: 43.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.085 M Tris-HCl pH 8.5, 0.17 M sodium acetate, 15% (v/v) glycerol, 27% (m/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99996 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 23, 2021 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99996 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 89852 / % possible obs: 95.3 % / Redundancy: 2 % / Biso Wilson estimate: 24.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.041 / Net I/σ(I): 11.99 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 13310 / CC1/2: 0.752 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Y2X, 1GFL Resolution: 1.8→46.18 Å / SU ML: 0.2232 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.5292 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: 26.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→46.18 Å
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Refine LS restraints |
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LS refinement shell |
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