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- PDB-6qvs: Unliganded structure of the human wild type Beta-galactoside alph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qvs | ||||||
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Title | Unliganded structure of the human wild type Beta-galactoside alpha-2,6-sialyltransferase 1 (ST6Gal1) | ||||||
![]() | Beta-galactoside alpha-2,6-sialyltransferase 1 | ||||||
![]() | TRANSFERASE / Sialyltransferase / Beta-galactoside alpha-2 / 6-sialyltransferase 1 / ST6Gal1 / N-linked glycosylation / apo | ||||||
Function / homology | ![]() beta-galactoside alpha-(2,6)-sialyltransferase / beta-galactoside alpha-2,6-sialyltransferase activity / Maturation of protein 3a / sialyltransferase activity / N-acetylneuraminate metabolic process / sialylation / Maturation of protein 3a / N-Glycan antennae elongation / Golgi trans cisterna / Termination of O-glycan biosynthesis ...beta-galactoside alpha-(2,6)-sialyltransferase / beta-galactoside alpha-2,6-sialyltransferase activity / Maturation of protein 3a / sialyltransferase activity / N-acetylneuraminate metabolic process / sialylation / Maturation of protein 3a / N-Glycan antennae elongation / Golgi trans cisterna / Termination of O-glycan biosynthesis / regulation of substrate adhesion-dependent cell spreading / O-glycan processing / negative regulation of chemotaxis / negative regulation of macrophage apoptotic process / Sialic acid metabolism / positive regulation of mononuclear cell proliferation / protein N-linked glycosylation via asparagine / Golgi medial cisterna / Golgi cisterna membrane / humoral immune response / response to ethanol / Maturation of spike protein / viral protein processing / Golgi membrane / Golgi apparatus / protein homodimerization activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Harrus, D. / Glumoff, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Unliganded and CMP-Neu5Ac bound structures of human alpha-2,6-sialyltransferase ST6Gal I at high resolution. Authors: Harrus, D. / Harduin-Lepers, A. / Glumoff, T. #1: ![]() Title: Unliganded and CMP-Neu5Ac bound structures of human alpha-2,6-sialyltransferase ST6Gal I at high resolution Authors: Harrus, D. / Harduin-Lepers, A. / Glumoff, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.4 KB | Display | ![]() |
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PDB format | ![]() | 103.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6qvtC ![]() 4js1S S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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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: 31803.148 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Compound details: residues 366-371 (chain A) and 366-370 (chain B) did not have clear electron density and were not traced Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P15907, beta-galactoside alpha-(2,6)-sialyltransferase #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.84 % / Description: 30-100 um prism-shaped plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Bis-Tris pH 5.5, 0.1 M Ammonium Acetate, 8% (w/v) PEG 20.000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→38.04 Å / Num. obs: 107819 / % possible obs: 98.86 % / Redundancy: 5 % / Rmerge(I) obs: 0.0456 / Rpim(I) all: 0.02301 / Rrim(I) all: 0.05124 / Net I/σ(I): 17.43 |
Reflection shell | Resolution: 1.6→1.657 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.6128 / Mean I/σ(I) obs: 2.28 / Num. unique obs: 10784 / Rpim(I) all: 0.3004 / Rrim(I) all: 0.6841 / % possible all: 99.09 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JS1 Resolution: 1.6→38.039 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.24 / 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: 73.77 Å2 / Biso mean: 29.3099 Å2 / Biso min: 13.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→38.039 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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