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Open data
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Basic information
Entry | Database: PDB / ID: 8y9p | ||||||
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Title | Crystal structure of bacterial activating sulfotransferase SgdX2 | ||||||
![]() | SgdX2 | ||||||
![]() | TRANSFERASE / sulfotransferase / SgdX2 | ||||||
Function / homology | Sulfotransferase, S. mansonii-type / Sulfotransferase domain / P-loop containing nucleoside triphosphate hydrolase / ADENOSINE-3'-5'-DIPHOSPHATE / SgdX2![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mori, T. / Teramoto, T. / Kakuta, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of activating sulfotransferase SgdX2 involved in biosynthesis of secondary metabolite sungeidine. Authors: Mori, T. / Teramoto, T. / Kakuta, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.8 KB | Display | ![]() |
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PDB format | ![]() | 77.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 16.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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
#1: Protein | Mass: 29153.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-A3P / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium chloride, 0.1 M Bis-Tris, pH 5.5, 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 4, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→48.61 Å / Num. obs: 33523 / % possible obs: 100 % / Redundancy: 14.3 % / CC1/2: 0.999 / Rrim(I) all: 0.06 / Net I/σ(I): 28.62 |
Reflection shell | Resolution: 1.64→1.73 Å / Mean I/σ(I) obs: 4.06 / Num. unique obs: 5400 / CC1/2: 0.857 / Rrim(I) all: 0.803 |
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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: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→48.61 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 30.8886 Å / Origin y: 13.1264 Å / Origin z: -0.7865 Å
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Refinement TLS group | Selection details: all |