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- PDB-7szh: Structure of the Rieske Non-heme Iron Oxygenase SxtT with beta-sa... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7szh | ||||||
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Title | Structure of the Rieske Non-heme Iron Oxygenase SxtT with beta-saxitoxinol Bound | ||||||
![]() | SxtT | ||||||
![]() | BIOSYNTHETIC PROTEIN / Saxitoxin GxtA Rieske oxygenase metalloprotein iron-sulfur cluster non-heme iron | ||||||
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. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Design principles for site-selective hydroxylation by a Rieske oxygenase. Authors: Liu, J. / Tian, J. / Perry, C. / Lukowski, A.L. / Doukov, T.I. / Narayan, A.R.H. / Bridwell-Rabb, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 260.2 KB | Display | ![]() |
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PDB format | ![]() | 190.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 11.5 MB | Display | ![]() |
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Full document | ![]() | 11.8 MB | Display | |
Data in XML | ![]() | 47.3 KB | Display | |
Data in CIF | ![]() | 68.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7szeC ![]() 7szfC ![]() 7szgC ![]() 6wn3S 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
-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 , 7 types, 868 molecules ![](data/chem/img/FES.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/D82.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/D82.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / #7: Chemical | #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: 3.05 Å3/Da / Density % sol: 59.68 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 2.0 M (NH4)2SO4, 0.1 M Bis-Tris pH 6.5, 10% v/v glycerol, 20 mM beta-saxitoxin |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50 Å / Num. obs: 129304 / % possible obs: 98.5 % / Redundancy: 13.7 % / Biso Wilson estimate: 33.84 Å2 / CC1/2: 1 / Rrim(I) all: 0.068 / Net I/σ(I): 22.05 |
Reflection shell | Resolution: 1.79→1.9 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 1.86 / Num. unique obs: 20590 / CC1/2: 0.815 / Rrim(I) all: 1.702 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6WN3 Resolution: 1.79→48.63 Å / SU ML: 0.2155 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2665 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→48.63 Å
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Refine LS restraints |
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LS refinement shell |
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