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Yorodumi- PDB-6h0b: Crystal structure of the human GalNAc-T4 in complex with UDP, man... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h0b | ||||||
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Title | Crystal structure of the human GalNAc-T4 in complex with UDP, manganese and the diglycopeptide 6. | ||||||
Components |
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Keywords | TRANSFERASE / GalNAc-Ts / GalNAc-T4 / short-range glycosylation preference / long-range glycosylation preference / (glyco)peptides / STD-NMR / Molecular dynamics / enzyme kinetics | ||||||
Function / homology | Function and homology information protein O-linked glycosylation via threonine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via serine / O-glycan processing / O-linked glycosylation of mucins / protein O-linked glycosylation / manganese ion binding / carbohydrate binding / Golgi membrane ...protein O-linked glycosylation via threonine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via serine / O-glycan processing / O-linked glycosylation of mucins / protein O-linked glycosylation / manganese ion binding / carbohydrate binding / Golgi membrane / perinuclear region of cytoplasm / extracellular exosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | de las Rivas, M. / Daniel, E.J.P. / Coelho, H. / Lira-Navarrete, E. / Raich, L. / Companon, I. / Diniz, A. / Lagartera, L. / Jimenez-Barbero, J. / Clausen, H. ...de las Rivas, M. / Daniel, E.J.P. / Coelho, H. / Lira-Navarrete, E. / Raich, L. / Companon, I. / Diniz, A. / Lagartera, L. / Jimenez-Barbero, J. / Clausen, H. / Rovira, C. / Marcelo, F. / Corzana, F. / Gerken, T.A. / Hurtado-Guerrero, R. | ||||||
Citation | Journal: ACS Cent Sci / Year: 2018 Title: Structural and Mechanistic Insights into the Catalytic-Domain-Mediated Short-Range Glycosylation Preferences of GalNAc-T4. Authors: de Las Rivas, M. / Paul Daniel, E.J. / Coelho, H. / Lira-Navarrete, E. / Raich, L. / Companon, I. / Diniz, A. / Lagartera, L. / Jimenez-Barbero, J. / Clausen, H. / Rovira, C. / Marcelo, F. / ...Authors: de Las Rivas, M. / Paul Daniel, E.J. / Coelho, H. / Lira-Navarrete, E. / Raich, L. / Companon, I. / Diniz, A. / Lagartera, L. / Jimenez-Barbero, J. / Clausen, H. / Rovira, C. / Marcelo, F. / Corzana, F. / Gerken, T.A. / Hurtado-Guerrero, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h0b.cif.gz | 254.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h0b.ent.gz | 199.4 KB | Display | PDB format |
PDBx/mmJSON format | 6h0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/6h0b ftp://data.pdbj.org/pub/pdb/validation_reports/h0/6h0b | HTTPS FTP |
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-Related structure data
Related structure data | 5nqaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 58 - 578 / Label seq-ID: 58 - 578
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-Components
-Protein / Protein/peptide / Sugars , 3 types, 5 molecules ABF
#1: Protein | Mass: 66755.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GALNT4 / Production host: Homo sapiens (human) References: UniProt: Q8N4A0, polypeptide N-acetylgalactosaminyltransferase #2: Protein/peptide | | Mass: 1199.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #7: Sugar | |
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-Non-polymers , 5 types, 828 molecules
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-MN / | #5: Chemical | ChemComp-UDP / | #6: Chemical | ChemComp-GOL / | #8: 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: 2.84 Å3/Da / Density % sol: 56.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG3350 ammonium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→73.99 Å / Num. obs: 133764 / % possible obs: 97.3 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rpim(I) all: 0.044 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 0.9 / CC1/2: 0.529 / Rpim(I) all: 0.742 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NQA Resolution: 1.8→73.99 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.767 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.152 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→73.99 Å
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Refine LS restraints |
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