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Yorodumi- 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 | |||||||||
Components | Sia-alpha-2,3-Gal-beta-1,4-GlcNAc-R:alpha 2,8-sialyltransferase | |||||||||
Keywords | TRANSFERASE / sialyltransferase / ternary complex / donor / acceptor | |||||||||
| Function / homology | Function and homology informationalpha-N-acetylneuraminate alpha-2,8-sialyltransferase / Transferases; Glycosyltransferases; Sialyltransferases / alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity / ganglioside biosynthetic process / 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 / alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity / ganglioside biosynthetic process / sialylation / glycosphingolipid biosynthetic process / N-Glycan antennae elongation / glycoprotein metabolic process / Sialic acid metabolism / sialic acid binding / oligosaccharide metabolic process / N-glycan processing / : / Golgi membrane / identical protein binding Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Volkers, G. / Worrall, L. / Strynadka, N.C.J. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2015Title: 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: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5bo9.cif.gz | 270.9 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb5bo9.ent.gz | 215.9 KB | Display | PDB format |
| PDBx/mmJSON format | 5bo9.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/5bo9 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/5bo9 | HTTPS FTP |
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-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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| 1 |
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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.) Homo sapiens (human) / Gene: ST8SIA3, SIAT8C / Plasmid: pFHMSP LIC N / Production host: ![]() References: UniProt: O43173, Transferases; Glycosyltransferases; Transferring other glycosyl groups |
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-Sugars , 4 types, 10 molecules 
| #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 


| #6: Chemical | | #7: Water | ChemComp-HOH / | |
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-Details
| Has protein modification | Y |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||
| 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: MOLECULAR REPLACEMENTStarting 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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Homo sapiens (human)
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