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- PDB-5bo9: Structure of human sialyltransferase ST8SiaIII in complex with CM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5bo9 | |||||||||
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Title | Structure of human sialyltransferase ST8SiaIII in complex with CMP-3FNeu5Ac and Sia-6S-LacNAc | |||||||||
![]() | Sia-alpha-2,3-Gal-beta-1,4-GlcNAc-R:alpha 2,8-sialyltransferase | |||||||||
![]() | TRANSFERASE / sialyltransferase / ternary complex / donor / acceptor | |||||||||
Function / homology | ![]() alpha-N-acetylneuraminate alpha-2,8-sialyltransferase / Transferases; Glycosyltransferases; Sialyltransferases / ganglioside biosynthetic process / alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity / sialylation / glycosphingolipid biosynthetic process / N-Glycan antennae elongation / glycoprotein metabolic process / Sialic acid metabolism / sialic acid binding ...alpha-N-acetylneuraminate alpha-2,8-sialyltransferase / Transferases; Glycosyltransferases; Sialyltransferases / ganglioside biosynthetic process / alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity / sialylation / glycosphingolipid biosynthetic process / N-Glycan antennae elongation / glycoprotein metabolic process / Sialic acid metabolism / sialic acid binding / oligosaccharide metabolic process / N-glycan processing / protein glycosylation / Golgi membrane / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Volkers, G. / Worrall, L. / Strynadka, N.C.J. | |||||||||
![]() | ![]() Title: Structure of human ST8SiaIII sialyltransferase provides insight into cell-surface polysialylation. Authors: Volkers, G. / Worrall, L.J. / Kwan, D.H. / Yu, C.C. / Baumann, L. / Lameignere, E. / Wasney, G.A. / Scott, N.E. / Wakarchuk, W. / Foster, L.J. / Withers, S.G. / Strynadka, N.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 271.2 KB | Display | ![]() |
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PDB format | ![]() | 215.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.3 MB | Display | ![]() |
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Full document | ![]() | 3.3 MB | Display | |
Data in XML | ![]() | 27.1 KB | Display | |
Data in CIF | ![]() | 36.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5bo6C ![]() 5bo7C ![]() 5bo8SC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 90 - 380 / Label seq-ID: 33 - 323
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Details | Dimer by SEC-MALS |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37919.012 Da / Num. of mol.: 2 / Fragment: UNP residues 81-380 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 4 types, 10 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | |
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-Non-polymers , 2 types, 175 molecules ![](data/chem/img/CSF.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 18-21% PEG3350, 30 mM sodium tartrate, 100 mM sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 21, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.3→75.89 Å / Num. obs: 34645 / % possible obs: 100 % / Redundancy: 4.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.044 / Net I/σ(I): 12.3 / Num. measured all: 166324 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5BO8 Resolution: 2.3→75.89 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 14.956 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.283 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.04 Å2 / Biso mean: 43.944 Å2 / Biso min: 20.47 Å2
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Refinement step | Cycle: final / Resolution: 2.3→75.89 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 16975 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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