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Yorodumi- PDB-8b6n: X-ray structure of the haloalkane dehalogenase HaloTag7 circular ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b6n | ||||||
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Title | X-ray structure of the haloalkane dehalogenase HaloTag7 circular permutated at positions 141-156 (cpHaloTagDelta) | ||||||
Components | Haloalkane dehalogenase | ||||||
Keywords | HYDROLASE / haloalkane dehalogenase / HaloTag / HaloTag7 / Self-Labeling Protein | ||||||
Function / homology | Haloalkane dehalogenase, subfamily 2 / haloalkane dehalogenase / haloalkane dehalogenase activity / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / response to toxic substance / Alpha/Beta hydrolase fold / Haloalkane dehalogenase Function and homology information | ||||||
Biological species | Rhodococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Tarnawski, M. / Johnsson, K. / Hiblot, J. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Science / Year: 2024 Title: Recording physiological history of cells with chemical labeling. Authors: Huppertz, M.C. / Wilhelm, J. / Grenier, V. / Schneider, M.W. / Falt, T. / Porzberg, N. / Hausmann, D. / Hoffmann, D.C. / Hai, L. / Tarnawski, M. / Pino, G. / Slanchev, K. / Kolb, I. / Acuna, ...Authors: Huppertz, M.C. / Wilhelm, J. / Grenier, V. / Schneider, M.W. / Falt, T. / Porzberg, N. / Hausmann, D. / Hoffmann, D.C. / Hai, L. / Tarnawski, M. / Pino, G. / Slanchev, K. / Kolb, I. / Acuna, C. / Fenk, L.M. / Baier, H. / 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 | 8b6n.cif.gz | 146.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b6n.ent.gz | 95.4 KB | Display | PDB format |
PDBx/mmJSON format | 8b6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/8b6n ftp://data.pdbj.org/pub/pdb/validation_reports/b6/8b6n | HTTPS FTP |
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-Related structure data
Related structure data | 8b6pC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32575.094 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-NHE / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.1 M CHES pH 9.5, 1.0 M trisodium citrate with 40% (v/v) polypropylene glycol P400 additive |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97797 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97797 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 12786 / % possible obs: 99.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 52.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.83 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1438 / CC1/2: 0.768 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Y2X Resolution: 2.3→39.7 Å / SU ML: 0.4627 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.2934 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: 57.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→39.7 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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