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Yorodumi- PDB-6zvu: X-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-P174L LAB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zvu | ||||||
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Title | X-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-P174L 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: 1.4 Å | ||||||
Authors | Tarnawski, M. / Frei, M. / Hiblot, J. / Johnsson, K. | ||||||
Citation | Journal: To Be Published Title: X-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-P174L LABELED WITH A CHLOROALKANE-TETRAMETHYLRHODAMINE FLUOROPHORE SUBSTRATE Authors: Tarnawski, M. / Frei, M. / 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 | 6zvu.cif.gz | 101.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zvu.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 6zvu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zvu_validation.pdf.gz | 363 KB | Display | wwPDB validaton report |
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Full document | 6zvu_full_validation.pdf.gz | 363.1 KB | Display | |
Data in XML | 6zvu_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 6zvu_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/6zvu ftp://data.pdbj.org/pub/pdb/validation_reports/zv/6zvu | HTTPS FTP |
-Related structure data
Related structure data | 6y7aS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33242.023 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-OEH / [ |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.39 % |
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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, 20% (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: 1.00006 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2019 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00006 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 63321 / % possible obs: 99.9 % / Redundancy: 6.48 % / Biso Wilson estimate: 11.62 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 6.22 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 7.55 / Num. unique obs: 11640 / CC1/2: 0.979 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Y7A Resolution: 1.4→45.76 Å / SU ML: 0.149 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.8667 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: 15.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→45.76 Å
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Refine LS restraints |
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LS refinement shell |
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