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Yorodumi- PDB-6egs: Crystal structure of the GalNAc-T2 F104S mutant in complex with U... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6egs | ||||||
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Title | Crystal structure of the GalNAc-T2 F104S mutant in complex with UDP-GalNAc | ||||||
Components | Polypeptide N-acetylgalactosaminyltransferase 2 | ||||||
Keywords | TRANSFERASE / F104S mutant / GalNAc-T2 / HDL / Glycosyltransferase / flexible loop / Inactive/Active states | ||||||
Function / homology | Function and homology information protein O-linked glycosylation via threonine / protein O-linked glycosylation via serine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / O-glycan processing / O-linked glycosylation of mucins / Golgi stack / COPI-independent Golgi-to-ER retrograde traffic / protein O-linked glycosylation / Golgi cisterna membrane ...protein O-linked glycosylation via threonine / protein O-linked glycosylation via serine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / O-glycan processing / O-linked glycosylation of mucins / Golgi stack / COPI-independent Golgi-to-ER retrograde traffic / protein O-linked glycosylation / Golgi cisterna membrane / protein maturation / manganese ion binding / carbohydrate binding / Golgi membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | de las Rivas, M. / Coelho, H. / Diniz, A. / Lira-Navarrete, E. / Jimenez-Barbero, J. / Schjoldager, K.T. / Bennett, E.P. / Vakhrushev, S.Y. / Clausen, H. / Corzana, F. ...de las Rivas, M. / Coelho, H. / Diniz, A. / Lira-Navarrete, E. / Jimenez-Barbero, J. / Schjoldager, K.T. / Bennett, E.P. / Vakhrushev, S.Y. / Clausen, H. / Corzana, F. / Marcelo, F. / Hurtado-Guerrero, R. | ||||||
Citation | Journal: Chemistry / Year: 2018 Title: Structural Analysis of a GalNAc-T2 Mutant Reveals an Induced-Fit Catalytic Mechanism for GalNAc-Ts. Authors: de Las Rivas, M. / Coelho, H. / Diniz, A. / Lira-Navarrete, E. / Companon, I. / Jimenez-Barbero, J. / Schjoldager, K.T. / Bennett, E.P. / Vakhrushev, S.Y. / Clausen, H. / Corzana, F. / ...Authors: de Las Rivas, M. / Coelho, H. / Diniz, A. / Lira-Navarrete, E. / Companon, I. / Jimenez-Barbero, J. / Schjoldager, K.T. / Bennett, E.P. / Vakhrushev, S.Y. / Clausen, H. / Corzana, F. / Marcelo, F. / 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 | 6egs.cif.gz | 394.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6egs.ent.gz | 322.9 KB | Display | PDB format |
PDBx/mmJSON format | 6egs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6egs_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6egs_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6egs_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 6egs_validation.cif.gz | 49.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/6egs ftp://data.pdbj.org/pub/pdb/validation_reports/eg/6egs | HTTPS FTP |
-Related structure data
Related structure data | 4d0tS 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: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 74 - 569 / Label seq-ID: 6 - 501
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-Components
#1: Protein | Mass: 57370.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GALNT2 / Production host: Komagataella pastoris (fungus) References: UniProt: Q10471, polypeptide N-acetylgalactosaminyltransferase #2: Chemical | #3: Chemical | #4: 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: 2.51 Å3/Da / Density % sol: 51.09 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG6000, Hepes |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→154.04 Å / Num. obs: 70380 / % possible obs: 99.7 % / Redundancy: 5.6 % / CC1/2: 0.995 / Rpim(I) all: 0.064 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.1 / CC1/2: 0.371 / Rpim(I) all: 0.72 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4D0T Resolution: 2.7→154.04 Å / SU B: 31.369 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 0.698 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.516 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→154.04 Å
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Refine LS restraints |
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