[English] 日本語
Yorodumi- PDB-7ziw: X-ray structure of the haloalkane dehalogenase HaloTag7 bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ziw | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of the haloalkane dehalogenase HaloTag7 bound to a butyltrifluoromethanesulfonamide tetramethylrhodamine ligand (TMR-T4) | ||||||
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: 1.99 Å | ||||||
Authors | Tarnawski, M. / Kompa, J. / Johnsson, K. / Hiblot, J. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: To Be Published Title: X-ray structure of the haloalkane dehalogenase HaloTag7 bound to a butyltrifluoromethanesulfonamide tetramethylrhodamine ligand (FSAm(4)-TMR) Authors: Tarnawski, M. / Kompa, J. / Johnsson, K. / Hiblot, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ziw.cif.gz | 155.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ziw.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ziw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/7ziw ftp://data.pdbj.org/pub/pdb/validation_reports/zi/7ziw | HTTPS FTP |
---|
-Related structure data
Related structure data | 6y7aS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-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 | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.82 % |
---|---|
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 |
---|---|
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: 1.99→50 Å / Num. obs: 30065 / % possible obs: 75.1 % / Redundancy: 2.06 % / Biso Wilson estimate: 10.09 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.093 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.99→2.07 Å / Redundancy: 2.18 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1504 / CC1/2: 0.844 / % possible all: 32.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Y7A Resolution: 1.99→44.68 Å / SU ML: 0.2554 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.1827 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→44.68 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|