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Yorodumi- PDB-5mek: Sulphotransferase-18 from Arabidopsis thaliana in complex with 3'... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mek | |||||||||
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Title | Sulphotransferase-18 from Arabidopsis thaliana in complex with 3'-phosphoadenosine 5'-phosphate (PAP) | |||||||||
Components | Cytosolic sulfotransferase 18 | |||||||||
Keywords | TRANSFERASE / Sulphotransferases / glucosinolate-biosynthesis / catalysis | |||||||||
Function / homology | Function and homology information aliphatic desulfoglucosinolate sulfotransferase / 3-methylthiopropyl-desulfoglucosinolate sulfotransferase activity / 4-methylthiobutyl-desulfoglucosinolate sulfotransferase activity / 5-methylthiopentyl-desulfoglucosinolate sulfotransferase activity / 7-methylthioheptyl-desulfoglucosinolate sulfotransferase activity / 8-methylthiooctyl-desulfoglucosinolate sulfotransferase activity / indol-3-yl-methyl-desulfoglucosinolate sulfotransferase activity / glucosinolate biosynthetic process / desulfoglucosinolate sulfotransferase activity / sulfation / cytoplasm Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | |||||||||
Authors | Hirschmann, F. / Krause, F. / Baruch, P. / Chizhov, I. / Mueller, J.W. / Manstein, D.J. / Papenbrock, J. / Fedorov, R. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Sci Rep / Year: 2017 Title: Structural and biochemical studies of sulphotransferase 18 from Arabidopsis thaliana explain its substrate specificity and reaction mechanism. Authors: Hirschmann, F. / Krause, F. / Baruch, P. / Chizhov, I. / Mueller, J.W. / Manstein, D.J. / Papenbrock, J. / Fedorov, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mek.cif.gz | 92.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mek.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 5mek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/5mek ftp://data.pdbj.org/pub/pdb/validation_reports/me/5mek | HTTPS FTP |
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-Related structure data
Related structure data | 5mexC 1q44S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37499.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SOT18, ST5B, At1g74090, F2P9.4 / Production host: Escherichia coli (E. coli) References: UniProt: Q9C9C9, Transferases; Transferring sulfur-containing groups; Sulfotransferases | ||||
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#2: Chemical | ChemComp-A3P / | ||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-POL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.48 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion / pH: 5.9 Details: 0.1 M MES pH 5.9, 16.5% PEG4000, 160 mM NaCl and 5% 1-propanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.91 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 12, 2014 Details: Pt coated mirrors in a Kirkpatrick-Baez geometry as the focusing system |
Radiation | Monochromator: horizontally diffracting Si (111) monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→45.85 Å / Num. obs: 42500 / % possible obs: 100 % / Redundancy: 21.66 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.0927 / Rsym value: 0.0275 / Net I/σ(I): 20.44 |
Reflection shell | Resolution: 1.74→1.84 Å / Redundancy: 22.33 % / Rmerge(I) obs: 0.7532 / Mean I/σ(I) obs: 2.65 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB-ID: 1Q44 Resolution: 1.74→19.99 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.203 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||
Displacement parameters | Biso mean: 30.185 Å2
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Refinement step | Cycle: 1 / Resolution: 1.74→19.99 Å
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Refine LS restraints | Type: r_scangle_other / Dev ideal: 5.666 / Dev ideal target: 4.366 / Number: 2217 | ||||||||||||||||||||
LS refinement shell | Resolution: 1.74→1.785 Å / Total num. of bins used: 20
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