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Yorodumi- PDB-7pcw: X-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-M175W LAB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pcw | ||||||
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Title | X-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-M175W LABELED WITH A CHLOROALKANE-TETRAMETHYLRHODAMINE FLUOROPHORE SUBSTRATE | ||||||
Components | Haloalkane dehalogenase | ||||||
Keywords | HYDROLASE / HALOALKANE DEHALOGENASE / HALO / TAG / 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: 2.3 Å | ||||||
Authors | Tarnawski, M. / Frei, M. / Hiblot, J. / Johnsson, K. | ||||||
Funding support | 1items
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Citation | Journal: Nat.Methods / Year: 2022 Title: Engineered HaloTag variants for fluorescence lifetime multiplexing. Authors: Frei, M.S. / Tarnawski, M. / Roberti, M.J. / Koch, B. / 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 | 7pcw.cif.gz | 300.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pcw.ent.gz | 195.8 KB | Display | PDB format |
PDBx/mmJSON format | 7pcw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/7pcw ftp://data.pdbj.org/pub/pdb/validation_reports/pc/7pcw | HTTPS FTP |
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-Related structure data
Related structure data | 6zvyC 7pcxC 6y7aS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 33280.996 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Gene: dhaA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A3G3, haloalkane dehalogenase #2: Chemical | ChemComp-OEH / [ #3: Chemical | ChemComp-CL / #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: 1.98 Å3/Da / Density % sol: 37.92 % |
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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: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 26, 2021 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 43477 / % possible obs: 95.6 % / Redundancy: 2.67 % / Biso Wilson estimate: 28.14 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.098 / Net I/σ(I): 8.44 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 2.58 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 5246 / CC1/2: 0.769 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Y7A Resolution: 2.3→40.36 Å / SU ML: 0.2773 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.3785 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: 29.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→40.36 Å
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Refine LS restraints |
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LS refinement shell |
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