+Open data
-Basic information
Entry | Database: PDB / ID: 6sp5 | ||||||||||||
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Title | Structure of hyperstable haloalkane dehalogenase variant DhaA115 | ||||||||||||
Components | Haloalkane dehalogenase | ||||||||||||
Keywords | HYDROLASE / Haloalkane dehalogenase | ||||||||||||
Function / homology | Function and homology information haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance Similarity search - Function | ||||||||||||
Biological species | Rhodococcus rhodochrous (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||||||||
Authors | Chmelova, K. / Markova, K. / Damborsky, J. / Marek, M. | ||||||||||||
Funding support | Czech Republic, 3items
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Citation | Journal: Chem Sci / Year: 2020 Title: Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst. Authors: Markova, K. / Chmelova, K. / Marques, S.M. / Carpentier, P. / Bednar, D. / 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 | 6sp5.cif.gz | 147.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sp5.ent.gz | 113.2 KB | Display | PDB format |
PDBx/mmJSON format | 6sp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sp/6sp5 ftp://data.pdbj.org/pub/pdb/validation_reports/sp/6sp5 | HTTPS FTP |
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-Related structure data
Related structure data | 6sp8C 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
#1: Protein | Mass: 33400.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Gene: dhaA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3G2, haloalkane dehalogenase #2: Chemical | #3: Chemical | ChemComp-SCN / #4: Chemical | ChemComp-GOL / | #5: 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: 2.9 Å3/Da / Density % sol: 57.63 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: PEG3350, potassium isothiocyanate, Bis-tris propane |
-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: 0.860999 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: 0.860999 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.6→48.074 Å / Num. obs: 99102 / % possible obs: 98.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 17.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Net I/σ(I): 13.7 | ||||||||||||||||||||||||
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: 1.6→48.074 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.59
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.79 Å2 / Biso mean: 22.0951 Å2 / Biso min: 10.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→48.074 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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