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Yorodumi- PDB-5u6m: Crystal structure of UDP-glucosyltransferase, UGT74F2, with UDP a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u6m | ||||||
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Title | Crystal structure of UDP-glucosyltransferase, UGT74F2, with UDP and salicylic acid | ||||||
Components | UDP-glycosyltransferase 74F2 | ||||||
Keywords | TRANSFERASE / UDP-glucosyltransferase / salicylic acid / salicylic acid glucoside / salicylic acid 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 / Resolution: 2.568 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 | 5u6m.cif.gz | 362.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u6m.ent.gz | 301.9 KB | Display | PDB format |
PDBx/mmJSON format | 5u6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/5u6m ftp://data.pdbj.org/pub/pdb/validation_reports/u6/5u6m | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 50821.621 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 #2: Sugar | #3: Chemical | #4: Chemical | #5: 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: 2.36 Å3/Da / Density % sol: 47.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 22-26 % (w/v) PEG3350, 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: 1.0332 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→50 Å / Num. obs: 30702 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 68.6431469736 Å2 / Net I/σ(I): 0.086 |
Reflection shell | Resolution: 2.56→2.65 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.7 / % possible all: 98 |
-Processing
Software |
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Refinement | Resolution: 2.568→43.841 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.72 / 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: 2.568→43.841 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: 56.5102 Å / Origin y: 75.947 Å / Origin z: 59.1517 Å
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Refinement TLS group | Selection details: all |