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- PDB-5zm3: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AndA with prean... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zm3 | ||||||
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Title | Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AndA with preandiloid B | ||||||
![]() | Dioxygenase andA | ||||||
![]() | OXIDOREDUCTASE / Oxygenase | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakashima, Y. / Senda, T. | ||||||
![]() | ![]() Title: Structural and Computational Bases for Dramatic Skeletal Rearrangement in Anditomin Biosynthesis. Authors: Nakashima, Y. / Mitsuhashi, T. / Matsuda, Y. / Senda, M. / Sato, H. / Yamazaki, M. / Uchiyama, 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 | ![]() | 241.3 KB | Display | ![]() |
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PDB format | ![]() | 190.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5zm2C ![]() 5zm4C ![]() 5ybmS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33854.402 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A097ZPD5, 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-FE / #3: Chemical | ChemComp-AKG / #4: Chemical | ChemComp-9FR / ( #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% (w/v) PEG 3350, 200mM sodium tartrate, 20% DMF |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→47.35 Å / Num. obs: 65777 / % possible obs: 97.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.25→2.3 Å / Rmerge(I) obs: 0.513 / Num. unique obs: 4400 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5YBM Resolution: 2.25→47.293 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→47.293 Å
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Refine LS restraints |
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LS refinement shell |
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