[English] 日本語
Yorodumi- PDB-5bo7: Structure of human sialyltransferase ST8SiaIII in complex with CTP -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bo7 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of human sialyltransferase ST8SiaIII in complex with CTP | ||||||||||||
Components | Sia-alpha-2,3-Gal-beta-1,4-GlcNAc-R:alpha 2,8-sialyltransferase | ||||||||||||
Keywords | TRANSFERASE / sialyltransferase / CTP | ||||||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||||||||
Authors | Volkers, G. / Worrall, L. / Strynadka, N.C.J. | ||||||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2015 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5bo7.cif.gz | 262.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5bo7.ent.gz | 209.1 KB | Display | PDB format |
PDBx/mmJSON format | 5bo7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/5bo7 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/5bo7 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5bo6C 5bo8SC 5bo9C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 89 - 380 / Label seq-ID: 32 - 323
| ||||||||||||||||||
Details | Dimer by SEC-MALS |
-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: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: O43173, EC: 2.4.99.- |
---|
-Sugars , 3 types, 8 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 #5: Sugar | ChemComp-NAG / | |
---|
-Non-polymers , 2 types, 366 molecules
#4: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.52 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 0.2 M (NH4)3PO4, 50 mM PIPES, 18-22% PEG2000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97947 Å | |||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Apr 29, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.85→46.94 Å / Num. obs: 70613 / % possible obs: 95.8 % / Redundancy: 4.9 % / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.021 / Net I/σ(I): 21.7 / Num. measured all: 349276 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BO8 Resolution: 1.85→46.94 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.1841 / WRfactor Rwork: 0.1578 / FOM work R set: 0.854 / SU B: 5.048 / SU ML: 0.078 / SU R Cruickshank DPI: 0.1107 / SU Rfree: 0.1077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 117.58 Å2 / Biso mean: 35.902 Å2 / Biso min: 17.91 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→46.94 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Ens-ID: 1 / Number: 31814 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|