[English] 日本語
Yorodumi- PDB-6o88: Crystal Structure of UDP-dependent glucosyltransferases (UGT) fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o88 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of UDP-dependent glucosyltransferases (UGT) from Stevia rebaudiana in complex with UDP and rebaudioside A | ||||||
Components | UDP-glycosyltransferase 76G1 | ||||||
Keywords | TRANSFERASE / plant biochemistry | ||||||
Function / homology | Function and homology information UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases Similarity search - Function | ||||||
Biological species | Stevia rebaudiana (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å | ||||||
Authors | Lee, S.G. / Jez, J.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Molecular basis for branched steviol glucoside biosynthesis. Authors: Lee, S.G. / Salomon, E. / Yu, O. / Jez, J.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6o88.cif.gz | 197.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6o88.ent.gz | 155.9 KB | Display | PDB format |
PDBx/mmJSON format | 6o88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/6o88 ftp://data.pdbj.org/pub/pdb/validation_reports/o8/6o88 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 52087.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stevia rebaudiana (plant) / Gene: UGT76G1 / Production host: Escherichia coli (E. coli) References: UniProt: Q6VAB4, Transferases; Glycosyltransferases; Hexosyltransferases |
---|---|
#2: Chemical | ChemComp-UDP / |
#3: Chemical | ChemComp-LRV / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.62 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 15% (w/v) PEG-4000, 20% 2-propanol (v/v), 100 mM sodium citrate tribasic dihydrate buffer pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→42.5 Å / Num. obs: 35139 / % possible obs: 99.5 % / Redundancy: 4.7 % / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 1.99→2.02 Å / Num. unique obs: 35139 / Rpim(I) all: 0.04 / Rsym value: 0.093 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.99→42.49 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.29
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→42.49 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|