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Yorodumi- PDB-8k9y: Crystal structure of Arabidopsis thaliana sulfotransferase SOT16 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8k9y | ||||||
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Title | Crystal structure of Arabidopsis thaliana sulfotransferase SOT16 involved in glucosinolate biosynthesis | ||||||
Components | Cytosolic sulfotransferase 16 | ||||||
Keywords | TRANSFERASE / sulfotransferase / sulfation | ||||||
Function / homology | Function and homology information aromatic desulfoglucosinolate sulfotransferase / response to jasmonic acid stimulus involved in jasmonic acid and ethylene-dependent systemic resistance / glucosinolate biosynthetic process / desulfoglucosinolate sulfotransferase activity / sulfation / mitochondrion / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Iwamoto, Y. / Saito, S. / Teramoto, T. / Kakuta, Y. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2023 Title: Crystal structure of Arabidopsis thaliana sulfotransferase SOT16 involved in glucosinolate biosynthesis. Authors: Iwamoto, Y. / Saito, S. / Teramoto, T. / Maruyama-Nakashita, A. / Kakuta, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k9y.cif.gz | 314.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k9y.ent.gz | 251.9 KB | Display | PDB format |
PDBx/mmJSON format | 8k9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k9y_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8k9y_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8k9y_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 8k9y_validation.cif.gz | 52.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/8k9y ftp://data.pdbj.org/pub/pdb/validation_reports/k9/8k9y | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37634.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SOT16 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9C9D0 |
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-Non-polymers , 5 types, 756 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-IPA / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.34 % |
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Crystal grow | Temperature: 293.4 K / Method: vapor diffusion, sitting drop / Details: PEG |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→47.58 Å / Num. obs: 73012 / % possible obs: 95 % / Redundancy: 3.32 % / CC1/2: 0.99 / Net I/σ(I): 8.28 |
Reflection shell | Resolution: 1.82→1.95 Å / Num. unique obs: 7301 / CC1/2: 0.746 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→47.58 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.82 / Stereochemistry target values: ML
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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: 1.82→47.58 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: -19.4485 Å / Origin y: 19.8376 Å / Origin z: 16.2756 Å
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Refinement TLS group | Selection details: all |