+Open data
-Basic information
Entry | Database: PDB / ID: 6iwr | ||||||
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Title | Crystal structure of GalNAc-T7 with UDP, GalNAc and Mn2+ | ||||||
Components | N-acetylgalactosaminyltransferase 7 | ||||||
Keywords | TRANSFERASE / Polypeptide N Acetylgalactosaminyltransferase Activity / Transferring Glycosyl Groups / Manganese Ion Binding / Carbohydrate Binding / Metal Ion Binding | ||||||
Function / homology | Function and homology information polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / O-glycan processing / O-linked glycosylation of mucins / protein O-linked glycosylation / carbohydrate binding / carbohydrate metabolic process / Golgi membrane / Golgi apparatus / extracellular exosome ...polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / O-glycan processing / O-linked glycosylation of mucins / protein O-linked glycosylation / carbohydrate binding / carbohydrate metabolic process / Golgi membrane / Golgi apparatus / extracellular exosome / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.604 Å | ||||||
Authors | Yu, C. / Yin, Y.X. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2019 Title: Structural basis of carbohydrate transfer activity of UDP-GalNAc: Polypeptide N-acetylgalactosaminyltransferase 7. Authors: Yu, C. / Liang, L. / Yin, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iwr.cif.gz | 660.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iwr.ent.gz | 547.2 KB | Display | PDB format |
PDBx/mmJSON format | 6iwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/6iwr ftp://data.pdbj.org/pub/pdb/validation_reports/iw/6iwr | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 7 molecules ABCDEF
#1: Protein | Mass: 68864.211 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GALNT7 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q86SF2, Transferases; Glycosyltransferases; Hexosyltransferases #3: Sugar | ChemComp-NAG / | |
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-Non-polymers , 4 types, 415 molecules
#2: Chemical | ChemComp-MN / #4: Chemical | ChemComp-UDP / | #5: Chemical | ChemComp-UD2 / | #6: Water | ChemComp-HOH / | |
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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: 3.31 Å3/Da / Density % sol: 62.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M Lithium sulfate monohydrate, 12%(w/v) Polyethylene glycol 4,000, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 5mM UDP, 5mM MnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.604→49.251 Å / Num. obs: 160537 / % possible obs: 96 % / Redundancy: 6.7 % / Net I/σ(I): 12.75 |
Reflection shell | Resolution: 2.604→2.697 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.604→49.251 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.55
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.604→49.251 Å
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Refine LS restraints |
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LS refinement shell |
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