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- PDB-8qfm: Ergothioneine dioxygenase from Thermocatellispora tengchongensis ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qfm | ||||||
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Title | Ergothioneine dioxygenase from Thermocatellispora tengchongensis in complex with manganese | ||||||
![]() | Cysteine dioxygenase | ||||||
![]() | OXIDOREDUCTASE / thiol dioxygenase Ergothioneine Dioxygenase | ||||||
Function / homology | ![]() oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / iron ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vasseur, C.M. / Seebeck, F.P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Enzyme-Catalyzed Oxidative Degradation of Ergothioneine. Authors: Nalivaiko, E.Y. / Vasseur, C.M. / Seebeck, F.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130 KB | Display | ![]() |
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PDB format | ![]() | 101.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.6 MB | Display | ![]() |
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Full document | ![]() | 4.6 MB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 21.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qflC ![]() 8qfnC ![]() 8qfoC ![]() 8qfpC ![]() 8qfqC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 20704.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: HNP84_002159 / Production host: ![]() ![]() |
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-Non-polymers , 7 types, 188 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/PEO.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEO.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PG4 / | #7: Chemical | ChemComp-PEG / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M magnesium acetate tetrahydrate 0.1 M sodium cacodylate, pH 6.5 20% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.38 Å / Num. obs: 57347 / % possible obs: 99.74 % / Redundancy: 2 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 14.51 |
Reflection shell | Resolution: 1.9→1.968 Å / Mean I/σ(I) obs: 1.96 / Num. unique obs: 5521 / CC1/2: 0.793 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→44.38 Å
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Refine LS restraints |
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LS refinement shell |
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