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Yorodumi- PDB-5lka: Crystal structure of haloalkane dehalogenase LinB 140A+143L+177W+... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lka | ||||||
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Title | Crystal structure of haloalkane dehalogenase LinB 140A+143L+177W+211L mutant (LinB86) from Sphingobium japonicum UT26 at 1.3 A resolution | ||||||
Components | Haloalkane dehalogenase | ||||||
Keywords | HYDROLASE / haloalkane dehalogenase / bacterial enzyme / mutant | ||||||
Function / homology | Function and homology information haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance / periplasmic space Similarity search - Function | ||||||
Biological species | Sphingobium japonicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.298 Å | ||||||
Authors | Degtjarik, O. / Rezacova, P. / Iermak, I. / Chaloupkova, R. / Damborsky, J. / Kuta Smatanova, I. | ||||||
Citation | Journal: Acs Catalysis / Year: 2016 Title: Engineering a de novo transport tunnel. Authors: Brezovsky, J. / Babkova, P. / Degtjarik, O. / Fortova, A. / Gora, A. / Iermak, I. / Rezacova, P. / Dvorak, P. / Kuta Smatanova, I. / Prokop, Z. / Chaloupkova, R. / Damborsky, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lka.cif.gz | 151.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lka.ent.gz | 118.4 KB | Display | PDB format |
PDBx/mmJSON format | 5lka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/5lka ftp://data.pdbj.org/pub/pdb/validation_reports/lk/5lka | HTTPS FTP |
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-Related structure data
Related structure data | 4wdrS 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: 33766.184 Da / Num. of mol.: 1 / Mutation: W140A, F143L, L177W, I211L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingobium japonicum (bacteria) / Gene: linB, dhaA, SJA_C1-19590 / Production host: Escherichia coli (E. coli) / References: UniProt: D4Z2G1, haloalkane dehalogenase |
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#2: Chemical | ChemComp-SCN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium thiocyanate, 20 % (w/v) PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.298→46.87 Å / Num. obs: 64480 / % possible obs: 99.6 % / Redundancy: 6.35 % / Biso Wilson estimate: 14.49 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 16.45 |
Reflection shell | Resolution: 1.298→1.38 Å / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 3.5 / % possible all: 98.7 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WDR Resolution: 1.298→40.522 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.13
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.72 Å2 / Biso mean: 12.6853 Å2 / Biso min: 4.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.298→40.522 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
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