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- PDB-6ldq: Sucrose-phosphate synthase (tll1590)_27_220_406_426_from Thermosy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ldq | ||||||
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Title | Sucrose-phosphate synthase (tll1590)_27_220_406_426_from Thermosynechococcus elongatus (twinned) | ||||||
![]() | Tll1590 protein | ||||||
![]() | 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 / THIOCYANATE ION / Tll1590 protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Su, J. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.9 KB | Display | ![]() |
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PDB format | ![]() | 129.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6kihSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24976.361 Da / Num. of mol.: 4 / Mutation: 221-405 deletion Source method: isolated from a genetically manipulated source Details: deletion of residues 221-405 in Q8DIJ5 Source: (gene. exp.) ![]() ![]() Gene: tll1590 / Production host: ![]() ![]() #2: Chemical | ChemComp-SCN / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 31, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→19.4 Å / Num. obs: 60298 / % possible obs: 99 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.92→1.97 Å / Rmerge(I) obs: 0.625 / Num. unique obs: 4059 |
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Processing
Software | Name: PHENIX / Version: 1.16_3549 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 6KIH Resolution: 1.92→19.398 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.22 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.68 Å2 / Biso mean: 25.4208 Å2 / Biso min: 9.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.92→19.398 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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