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Yorodumi- PDB-5lv9: Crystal structure of thermophilic tryptophan halogenase (Th-Hal) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lv9 | ||||||
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Title | Crystal structure of thermophilic tryptophan halogenase (Th-Hal) enzyme from Streptomycin violaceusniger. | ||||||
Components | thermophilic tryptophan halogenase | ||||||
Keywords | HYDROLASE / thermophilic / flavin reductase / enzyme | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces violaceusniger (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.33 Å | ||||||
Authors | Dunstan, M.S. / Menon, B. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Org.Biomol.Chem. / Year: 2016 Title: Structure and biocatalytic scope of thermophilic flavin-dependent halogenase and flavin reductase enzymes. Authors: Menon, B.R. / Latham, J. / Dunstan, M.S. / Brandenburger, E. / Klemstein, U. / Leys, D. / Karthikeyan, C. / Greaney, M.F. / Shepherd, S.A. / Micklefield, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lv9.cif.gz | 411.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lv9.ent.gz | 351.4 KB | Display | PDB format |
PDBx/mmJSON format | 5lv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/5lv9 ftp://data.pdbj.org/pub/pdb/validation_reports/lv/5lv9 | HTTPS FTP |
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-Related 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: 57969.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces violaceusniger (bacteria) / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A1L1QK36*PLUS #2: Water | ChemComp-HOH / | |
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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: 2.68 Å3/Da / Density % sol: 54.09 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.06 M divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dehydrate) in 0.1 M buffer (1.0M imidazole + MES monohydrate acid buffer) at pH 6.5 made up with a 50% v/v ...Details: 0.06 M divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dehydrate) in 0.1 M buffer (1.0M imidazole + MES monohydrate acid buffer) at pH 6.5 made up with a 50% v/v precipitant mix (that contained 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350). |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→57.7 Å / Num. obs: 51611 / % possible obs: 99.7 % / Redundancy: 9.9 % / Net I/σ(I): 11.7 |
-Processing
Software |
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Refinement | Resolution: 2.33→56.493 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.17 Å2 / Biso mean: 43.1279 Å2 / Biso min: 17.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.33→56.493 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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