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- PDB-5ybn: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase PrhA in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ybn | ||||||
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Title | Fe(II)/(alpha)ketoglutarate-dependent dioxygenase PrhA in complex with (alpha)ketoglutarate | ||||||
![]() | PrhA | ||||||
![]() | OXIDOREDUCTASE / alpha-kegoglutarate-dependent dioxygenase | ||||||
Function / homology | paraherquonin 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 / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / dioxygenase activity / metal ion binding / 2-OXOGLUTARIC ACID / : / Multifunctional dioxygenase prhA![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakashima, Y. / Senda, M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.8 KB | Display | ![]() |
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PDB format | ![]() | 102.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.8 KB | Display | ![]() |
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Full document | ![]() | 449.8 KB | Display | |
Data in XML | ![]() | 25.5 KB | Display | |
Data in CIF | ![]() | 36.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yblC ![]() 5ybmSC ![]() 5yboC ![]() 5ybpC ![]() 5ybqC ![]() 5ybrC ![]() 5ybsC ![]() 5ybtC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35166.781 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 6-294 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, lithium citrate |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 4, 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→43.1 Å / Num. obs: 44951 / % possible obs: 99.6 % / Redundancy: 3.5 % / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.1→2.2 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5YBM Resolution: 2.104→43.087 Å / Cross valid method: FREE R-VALUE / Phase error: 24.52
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.104→43.087 Å
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Refine LS restraints |
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LS refinement shell |
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