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Yorodumi- PDB-5v2k: Crystal structure of UDP-glucosyltransferase, UGT74F2 (T15A), wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v2k | |||||||||
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Title | Crystal structure of UDP-glucosyltransferase, UGT74F2 (T15A), with UDP and 2-bromobenzoic acid | |||||||||
Components | UDP-glycosyltransferase 74F2 | |||||||||
Keywords | TRANSFERASE / UDP-glucosyltransferase / Salicylic acid / Salicylic acid glucoside / Salicylic acid glucose ester | |||||||||
Function / homology | Function and homology information para-aminobenzoic acid metabolic process / salicylic acid glucosyltransferase (ester-forming) activity / salicylic acid glucosyltransferase (glucoside-forming) activity / benzoic acid glucosyltransferase activity / UDP-glucose:4-aminobenzoate acylglucosyltransferase activity / nicotinate-O-glucosyltransferase activity / salicylic acid metabolic process / positive regulation of seed germination / benzoate metabolic process / UDP-glucosyltransferase activity ...para-aminobenzoic acid metabolic process / salicylic acid glucosyltransferase (ester-forming) activity / salicylic acid glucosyltransferase (glucoside-forming) activity / benzoic acid glucosyltransferase activity / UDP-glucose:4-aminobenzoate acylglucosyltransferase activity / nicotinate-O-glucosyltransferase activity / salicylic acid metabolic process / positive regulation of seed germination / benzoate metabolic process / UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / cytosol Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å | |||||||||
Authors | George Thompson, A.M. / Iancu, C.V. / Dean, J.V. / Choe, J. | |||||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Differences in salicylic acid glucose conjugations by UGT74F1 and UGT74F2 from Arabidopsis thaliana. Authors: George Thompson, A.M. / Iancu, C.V. / Neet, K.E. / Dean, J.V. / Choe, J.Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v2k.cif.gz | 374.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v2k.ent.gz | 302.8 KB | Display | PDB format |
PDBx/mmJSON format | 5v2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/5v2k ftp://data.pdbj.org/pub/pdb/validation_reports/v2/5v2k | HTTPS FTP |
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-Related structure data
Related structure data | 5u6mSC 5u6nC 5u6sC 5v2jC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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: 50791.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: UGT74F2, GT, SAGT1, SGT1, At2g43820, F18O19.7 / Production host: Escherichia coli (E. coli) References: UniProt: O22822, Transferases; Glycosyltransferases; Hexosyltransferases |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | #3: Sugar | |
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-Non-polymers , 3 types, 120 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.28 Å3/Da / Density % sol: 45.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 22-26 % (w/v) PEG 3350. 0.2 M ammonium acetate, 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97972 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97972 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 63121 / % possible obs: 100 % / Redundancy: 6.8 % / Net I/σ(I): 29.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5U6M Resolution: 2.002→43.927 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.08 / 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: 2.002→43.927 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: -10.1961 Å / Origin y: -8.1763 Å / Origin z: 17.997 Å
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Refinement TLS group | Selection details: all |