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Yorodumi- PDB-6xy9: Crystal structure of haloalkane dehalogenase DbeA-M1 loop variant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xy9 | |||||||||||||||
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Title | Crystal structure of haloalkane dehalogenase DbeA-M1 loop variant from Bradyrhizobium elkanii | |||||||||||||||
Components | Haloalkane dehalogenase | |||||||||||||||
Keywords | HYDROLASE / Haloalakane dehalogenase / microbial hydrolase / loop-helix engineering | |||||||||||||||
Function / homology | Haloalkane dehalogenase, subfamily 2 / haloalkane dehalogenase / haloalkane dehalogenase activity / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / ACETATE ION / Haloalkane dehalogenase Function and homology information | |||||||||||||||
Biological species | Bradyrhizobium elkanii USDA 94 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||||||||
Authors | Prudnikova, T. / Rezacova, P. / Kuta Smatanova, I. / Chaloupkova, R. / Damborsky, J. | |||||||||||||||
Funding support | Czech Republic, 4items
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Citation | Journal: Comput Struct Biotechnol J / Year: 2020 Title: Structural and catalytic effects of surface loop-helix transplantation within haloalkane dehalogenase family. Authors: Marek, M. / Chaloupkova, R. / Prudnikova, T. / Sato, Y. / Rezacova, P. / Nagata, Y. / Kuta Smatanova, I. / Damborsky, J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xy9.cif.gz | 135.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xy9.ent.gz | 104.7 KB | Display | PDB format |
PDBx/mmJSON format | 6xy9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/6xy9 ftp://data.pdbj.org/pub/pdb/validation_reports/xy/6xy9 | HTTPS FTP |
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-Related structure data
Related structure data | 4k2aS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 33731.242 Da / Num. of mol.: 2 / Mutation: 143VAEEQDHAE Source method: isolated from a genetically manipulated source Details: artifitially synthesized Source: (gene. exp.) Bradyrhizobium elkanii USDA 94 (bacteria) Gene: dbeA, dhaA / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / References: UniProt: E2RV62, haloalkane dehalogenase #2: Chemical | ChemComp-CL / #3: Chemical | #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: 2.89 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG 4000, 130 mM calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.918 Å |
Detector | Type: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Jan 16, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→19.6 Å / Num. obs: 38810 / % possible obs: 98.6 % / Redundancy: 3.74 % / Biso Wilson estimate: 32.3 Å2 / CC1/2: 0.86 / Rmerge(I) obs: 0.138 / Net I/σ(I): 11.76 |
Reflection shell | Resolution: 2.2→2.27 Å / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 3.35 / Num. unique obs: 6037 / CC1/2: 0.628 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4k2a Resolution: 2.2→19.6 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.459 / SU ML: 0.136 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.196 / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.2 Å2 / Biso mean: 31.675 Å2 / Biso min: 12.16 Å2
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Refinement step | Cycle: final / Resolution: 2.2→19.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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