+Open data
-Basic information
Entry | Database: PDB / ID: 5ybl | ||||||
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Title | Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AusE | ||||||
Components | Multifunctional dioxygenase ausE | ||||||
Keywords | OXIDOREDUCTASE / alpha-kegoglutarate-dependent dioxygenase | ||||||
Function / homology | Function and homology information austinol biosynthetic process / dehydroaustinol biosynthetic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / terpenoid biosynthetic process / dioxygenase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Emericella nidulans (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.108 Å | ||||||
Authors | Nakashima, Y. / Senda, M. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Structure function and engineering of multifunctional non-heme iron dependent oxygenases in fungal meroterpenoid biosynthesis. Authors: Nakashima, Y. / Mori, T. / Nakamura, H. / Awakawa, T. / Hoshino, S. / Senda, M. / Senda, T. / Abe, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ybl.cif.gz | 217 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ybl.ent.gz | 170 KB | Display | PDB format |
PDBx/mmJSON format | 5ybl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/5ybl ftp://data.pdbj.org/pub/pdb/validation_reports/yb/5ybl | HTTPS FTP |
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-Related structure data
Related structure data | 5ybmC 5ybnC 5yboC 5ybpC 5ybqC 5ybrC 5ybsC 5ybtC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35143.730 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 6-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Emericella nidulans (mold) / Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: ausE, AN9246 / Production host: Escherichia coli (E. coli) References: UniProt: Q5AR34, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor #2: Chemical | ChemComp-MN / #3: Chemical | #4: 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: 2.36 Å3/Da / Density % sol: 47.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, sodium citrate |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48.414 Å / Num. obs: 75992 / % possible obs: 98.6 % / Redundancy: 6.8 % / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.1→2.14 Å |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.108→48.414 Å / Cross valid method: FREE R-VALUE / Phase error: 32.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.108→48.414 Å
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Refine LS restraints |
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LS refinement shell |
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