+Open data
-Basic information
Entry | Database: PDB / ID: 6nie | ||||||
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Title | BesD with Fe(II), chloride, and alpha-ketoglutarate | ||||||
Components | BesD, lysine halogenase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / halogenase | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and the other dehydrogenated / L-lysine 4-chlorinase activity / L-beta-ethynylserine biosynthetic process / L-propargylglycine biosynthetic process / amino acid biosynthetic process / antibiotic biosynthetic process Similarity search - Function | ||||||
Biological species | Streptomyces cattleya (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å | ||||||
Authors | Neugebauer, M.E. / Chang, M.C.Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2019 Title: A family of radical halogenases for the engineering of amino-acid-based products. Authors: Neugebauer, M.E. / Sumida, K.H. / Pelton, J.G. / McMurry, J.L. / Marchand, J.A. / Chang, M.C.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nie.cif.gz | 425.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nie.ent.gz | 348.3 KB | Display | PDB format |
PDBx/mmJSON format | 6nie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/6nie ftp://data.pdbj.org/pub/pdb/validation_reports/ni/6nie | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 29319.025 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces cattleya (strain ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057) (bacteria) Strain: ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057 Gene: SCATT_p06880 / Production host: Escherichia coli (E. coli) / References: UniProt: G8XHD5 |
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-Non-polymers , 6 types, 864 molecules
#2: Chemical | ChemComp-LYS / #3: Chemical | ChemComp-FE2 / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-AKG / #6: Chemical | ChemComp-FE / | #7: 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: 2.37 Å3/Da / Density % sol: 48.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 1:1 volume of protein solution (10 mg/mL BesD, lysine (1.5 mM), alpha-ketoglutarate (3 mM, pH 7)) and reservoir solution (MES pH 6.5 (100 mM), sodium chloride (0.6 mM), containing 20% (v/v) ...Details: 1:1 volume of protein solution (10 mg/mL BesD, lysine (1.5 mM), alpha-ketoglutarate (3 mM, pH 7)) and reservoir solution (MES pH 6.5 (100 mM), sodium chloride (0.6 mM), containing 20% (v/v) PEG 4000. Soaked anaerobically in a solution containing (NH4)2Fe(SO4)2 * 6H2O (1mM), alpha-ketoglutarate (1 mM), sodium ascorbate (1 mM), lysine (1 mM), and glycerol (20% (v/v) for 30 min before flash freezing in liquid nitrogen |
-Data collection
Diffraction | Mean temperature: 194 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→70.03 Å / Num. obs: 149915 / % possible obs: 97.35 % / Redundancy: 13.6 % / CC1/2: 0.998 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.95→2.02 Å / Num. unique obs: 7341 / CC1/2: 0.78 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.95→70.027 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→70.027 Å
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Refine LS restraints |
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LS refinement shell |
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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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