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Yorodumi- PDB-6xt8: Crystal structure of haloalkane dehalogenase variant DhaA115 doma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xt8 | ||||||
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Title | Crystal structure of haloalkane dehalogenase variant DhaA115 domain-swapped dimer type-2 | ||||||
Components | Haloalkane dehalogenase variant DhaA115 domain-swapped dimer type-2 | ||||||
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: 1.7 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 | 6xt8.cif.gz | 260.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xt8.ent.gz | 208.2 KB | Display | PDB format |
PDBx/mmJSON format | 6xt8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xt8_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 6xt8_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 6xt8_validation.xml.gz | 48 KB | Display | |
Data in CIF | 6xt8_validation.cif.gz | 69.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/6xt8 ftp://data.pdbj.org/pub/pdb/validation_reports/xt/6xt8 | HTTPS FTP |
-Related structure data
Related structure data | 6ty7C 6xtcC 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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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 34447.383 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, haloalkane dehalogenase |
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-Non-polymers , 5 types, 697 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-PG4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.52 Å3/Da / Density % sol: 51.16 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG 3350, ammonium nitrate, bis-tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.861 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.861 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→47 Å / Num. obs: 141424 / % possible obs: 97.8 % / Redundancy: 4.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.024 / Rrim(I) all: 0.053 / Net I/σ(I): 16 / Num. measured all: 652840 / Scaling rejects: 73 | ||||||||||||||||||||||||||||||
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: 1.7→45.528 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.93 Å2 / Biso mean: 28.2553 Å2 / Biso min: 12.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→45.528 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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