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Yorodumi- PDB-6s24: Crystal structure of the TgGalNAc-T3 in complex with UDP, mangane... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s24 | ||||||
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Title | Crystal structure of the TgGalNAc-T3 in complex with UDP, manganese and the peptide 3 | ||||||
Components |
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Keywords | TRANSFERASE / GalNAc-Ts / GalNAc-T3 / long-range glycosylation preference / (glyco)peptides / Molecular dynamics / specificity / enzyme kinetics / FGF23 / phosphate homeostasis | ||||||
Function / homology | Function and homology information protein O-linked glycosylation via threonine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / manganese ion binding / carbohydrate binding / Golgi membrane Similarity search - Function | ||||||
Biological species | Taeniopygia guttata (zebra finch) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | ||||||
Authors | de las Rivas, M. / Daniel, E.J.P. / Narimatsu, Y. / Companon, I. / Kato, K. / Hermosilla, P. / Thureau, A. / Ceballos-Laita, L. / Coelho, H. / Bernado, P. ...de las Rivas, M. / Daniel, E.J.P. / Narimatsu, Y. / Companon, I. / Kato, K. / Hermosilla, P. / Thureau, A. / Ceballos-Laita, L. / Coelho, H. / Bernado, P. / Marcelo, F. / Hansen, L. / Lostao, A. / Corzana, F. / Clausen, H. / Gerken, T.A. / Hurtado-Guerrero, R. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2020 Title: Molecular basis for fibroblast growth factor 23 O-glycosylation by GalNAc-T3. Authors: de Las Rivas, M. / Paul Daniel, E.J. / Narimatsu, Y. / Companon, I. / Kato, K. / Hermosilla, P. / Thureau, A. / Ceballos-Laita, L. / Coelho, H. / Bernado, P. / Marcelo, F. / Hansen, L. / ...Authors: de Las Rivas, M. / Paul Daniel, E.J. / Narimatsu, Y. / Companon, I. / Kato, K. / Hermosilla, P. / Thureau, A. / Ceballos-Laita, L. / Coelho, H. / Bernado, P. / Marcelo, F. / Hansen, L. / Maeda, R. / Lostao, A. / Corzana, F. / Clausen, H. / 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 | 6s24.cif.gz | 137.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s24.ent.gz | 102.5 KB | Display | PDB format |
PDBx/mmJSON format | 6s24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s24_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6s24_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6s24_validation.xml.gz | 26 KB | Display | |
Data in CIF | 6s24_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/6s24 ftp://data.pdbj.org/pub/pdb/validation_reports/s2/6s24 | HTTPS FTP |
-Related structure data
Related structure data | 6s22C 5nqaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AF
#1: Protein | Mass: 72365.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Taeniopygia guttata (zebra finch) / Gene: GALNT3 / Production host: Komagataella pastoris (fungus) References: UniProt: H0ZAB5, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: Protein/peptide | Mass: 1085.126 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: AT*GAGAGAGTTPGP Note that this is a monoglycopeptide and T* stands for T-O-GalNAc Source: (synth.) Homo sapiens (human) |
-Sugars , 2 types, 2 molecules
#7: Sugar | ChemComp-NAG / |
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#8: Sugar | ChemComp-NGA / |
-Non-polymers , 5 types, 220 molecules
#3: Chemical | ChemComp-TAM / | ||||||
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#4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-UDP / | #6: Chemical | ChemComp-MN / | #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | 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: 2.56 Å3/Da / Density % sol: 52.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: Morpheus precipitant mix 4, nitrate phosphate buffer and Morpheus buffer System 1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→20 Å / Num. obs: 41413 / % possible obs: 94 % / Redundancy: 5.3 % / CC1/2: 0.996 / Rpim(I) all: 0.051 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.12→2.23 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4490 / CC1/2: 0.522 / Rpim(I) all: 0.491 / % possible all: 71.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NQA Resolution: 2.12→19.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.459 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.181 / 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: 41.609 Å2
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Refinement step | Cycle: 1 / Resolution: 2.12→19.96 Å
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Refine LS restraints |
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