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- PDB-6wnb: Structure of the Rieske non-heme iron oxygenase SxtT with dideoxy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wnb | ||||||
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Title | Structure of the Rieske non-heme iron oxygenase SxtT with dideoxysaxitoxin bound | ||||||
![]() | SxtT | ||||||
![]() | BIOSYNTHETIC PROTEIN / saxitoxin / Rieske oxygenase / metalloprotein / natural products | ||||||
Function / homology | ![]() 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bridwell-Rabb, J. / Liu, J. | ||||||
![]() | ![]() Title: Structural basis for divergent C-H hydroxylation selectivity in two Rieske oxygenases. Authors: Lukowski, A.L. / Liu, J. / Bridwell-Rabb, J. / Narayan, A.R.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 247.1 KB | Display | ![]() |
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PDB format | ![]() | 181.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6wn3SC ![]() 6wncC ![]() 6wndC 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 on special symmetry positions |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 38432.648 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 471 molecules ![](data/chem/img/FES.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/U5A.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/U5A.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / #7: 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: 3.06 Å3/Da / Density % sol: 59.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2.0 M (NH4)2SO4, 0.1 M Bis-Tris pH 6.5, 10% v/v glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30.16 Å / Num. obs: 81796 / % possible obs: 98.4 % / Redundancy: 4.7 % / Biso Wilson estimate: 36.45 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.1→2.175 Å / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 8066 / CC1/2: 0.89 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6WN3 Resolution: 2.1→30.16 Å / SU ML: 0.2202 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.6312
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30.16 Å
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Refine LS restraints |
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LS refinement shell |
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