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Yorodumi- PDB-6xtc: Crystal structure of haloalkane dehalogenase variant DhaA177 doma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xtc | ||||||
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Title | Crystal structure of haloalkane dehalogenase variant DhaA177 domain-swapped dimer type-3 | ||||||
Components | Haloalkane dehalogenase variant DhaA177 domain-swapped dimer type-3 | ||||||
Keywords | HYDROLASE / Haloalkane dehalogenase | ||||||
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 | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.543 Å | ||||||
Authors | Markova, K. / Damborsky, J. / Marek, M. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: Acs Catalysis / Year: 2021 Title: Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers Authors: Markova, K. / Kunka, A. / Chmelova, K. / Havlasek, M. / Babkova, P. / Marques, S.M. / Vasina, M. / Planas-Iglesias, J. / Chaloupkova, R. / Bednar, D. / Prokop, Z. / Damborsky, J. / Marek, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xtc.cif.gz | 250.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xtc.ent.gz | 202.1 KB | Display | PDB format |
PDBx/mmJSON format | 6xtc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/6xtc ftp://data.pdbj.org/pub/pdb/validation_reports/xt/6xtc | HTTPS FTP |
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-Related structure data
Related structure data | 6ty7C 6xt8C 4hzgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34235.070 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3G2*PLUS #2: Chemical | #3: Chemical | ChemComp-SO4 / #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: 3.67 Å3/Da / Density % sol: 66.46 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Ammonium sulphate, lithium sulphate, tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 27, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99987 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.54→45.524 Å / Num. obs: 66790 / % possible obs: 99.8 % / Redundancy: 13.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.046 / Rrim(I) all: 0.169 / Net I/σ(I): 15.3 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HZG Resolution: 2.543→45.524 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.15
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.83 Å2 / Biso mean: 56.032 Å2 / Biso min: 18.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.543→45.524 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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