[English] 日本語
Yorodumi- PDB-6kih: Sucrose-phosphate synthase (tll1590) from Thermosynechococcus elo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kih | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Sucrose-phosphate synthase (tll1590) from Thermosynechococcus elongatus | |||||||||
Components | Tll1590 protein | |||||||||
Keywords | TRANSFERASE / Sucrose-phosphate synthase | |||||||||
Function / homology | Glycosyl transferase 4-like domain / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / sucrose-6-phosphate / URIDINE-5'-DIPHOSPHATE / Tll1590 protein Function and homology information | |||||||||
Biological species | Thermosynechococcus elongatus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Su, J. | |||||||||
Citation | Journal: Front Microbiol / Year: 2020 Title: Co-crystal Structure ofThermosynechococcus elongatusSucrose Phosphate Synthase With UDP and Sucrose-6-Phosphate Provides Insight Into Its Mechanism of Action Involving an Oxocarbenium Ion and the Glycosidic Bond. Authors: Li, Y. / Yao, Y. / Yang, G. / Tang, J. / Ayala, G.J. / Li, X. / Zhang, W. / Han, Q. / Yang, T. / Wang, H. / Mayo, K.H. / Su, J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6kih.cif.gz | 821.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6kih.ent.gz | 689.2 KB | Display | PDB format |
PDBx/mmJSON format | 6kih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/6kih ftp://data.pdbj.org/pub/pdb/validation_reports/ki/6kih | HTTPS FTP |
---|
-Related structure data
Related structure data | 6ldqC 3c4qS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
7 |
| ||||||||
8 |
| ||||||||
9 |
| ||||||||
10 |
| ||||||||
11 |
| ||||||||
12 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 50355.359 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus elongatus (bacteria) Gene: tll1590 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DIJ5 #2: Polysaccharide | 6-O-phosphono-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose-6-phosphate #3: Chemical | ChemComp-UDP / Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 58.55 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3→19.9 Å / Num. obs: 122717 / % possible obs: 98.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 3→3.06 Å / Rmerge(I) obs: 0.855 / Num. unique obs: 5683 |
-Processing
Software | Name: PHENIX / Version: 1.17_3644 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3c4q Resolution: 3→19.9 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.1 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 176.12 Å2 / Biso mean: 80.6966 Å2 / Biso min: 30 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→19.9 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
|