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Yorodumi- PDB-7zix: X-ray structure of the haloalkane dehalogenase HaloTag7 bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zix | ||||||
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Title | X-ray structure of the haloalkane dehalogenase HaloTag7 bound to a butylmethanesulfonamide tetramethylrhodamine ligand (TMR-S4) | ||||||
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: 2.39 Å | ||||||
Authors | Tarnawski, M. / Kompa, J. / Johnsson, K. / Hiblot, J. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: X-ray structure of the haloalkane dehalogenase HaloTag7 bound to a butylmethanesulfonamide tetramethylrhodamine ligand (HSAm(4)-TMR) Authors: Tarnawski, M. / Kompa, J. / 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 | 7zix.cif.gz | 153.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zix.ent.gz | 102.7 KB | Display | PDB format |
PDBx/mmJSON format | 7zix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/7zix ftp://data.pdbj.org/pub/pdb/validation_reports/zi/7zix | HTTPS FTP |
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-Related structure data
Related structure data | 6y7aS 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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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: 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: 2.13 Å3/Da / Density % sol: 42.18 % |
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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, 23% (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: 1.00007 Å |
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: 2.39→50 Å / Num. obs: 20776 / % possible obs: 93.5 % / Redundancy: 3.83 % / Biso Wilson estimate: 15.93 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.123 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.39→2.45 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1039 / CC1/2: 0.874 / % possible all: 68.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Y7A Resolution: 2.39→44.18 Å / SU ML: 0.2158 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.5197 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: 36.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.39→44.18 Å
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Refine LS restraints |
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LS refinement shell |
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