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Yorodumi- PDB-5ajp: Crystal structure of the active form of GalNAc-T2 in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ajp | |||||||||
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Title | Crystal structure of the active form of GalNAc-T2 in complex with UDP and the glycopeptide MUC5AC-13 | |||||||||
Components |
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Keywords | TRANSFERASE / GALNAC-T2 / AFM / SAXS / LECTIN DOMAIN / COARSE-GRAINED MODEL / GLYCOPEPTIDES / INACTIVE FORM / ACTIVE FORM / COMPACT FORM / EXTENDED FORM | |||||||||
Function / homology | Function and homology information mucus layer / protein O-linked glycosylation via threonine / protein O-linked glycosylation via serine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-glycan processing ...mucus layer / protein O-linked glycosylation via threonine / protein O-linked glycosylation via serine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-glycan processing / O-linked glycosylation of mucins / Golgi stack / COPI-independent Golgi-to-ER retrograde traffic / protein O-linked glycosylation / extracellular matrix structural constituent / Golgi cisterna membrane / Dectin-2 family / protein maturation / extracellular matrix / Golgi lumen / manganese ion binding / carbohydrate binding / Golgi membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Lira-Navarrete, E. / delasRivas, M. / Companon, I. / Pallares, M.C. / Kong, Y. / Iglesias-Fernandez, J. / Bernardes, G.J.L. / Peregrina, J.M. / Rovira, C. / Bernado, P. ...Lira-Navarrete, E. / delasRivas, M. / Companon, I. / Pallares, M.C. / Kong, Y. / Iglesias-Fernandez, J. / Bernardes, G.J.L. / Peregrina, J.M. / Rovira, C. / Bernado, P. / Bruscolini, P. / Clausen, H. / Lostao, A. / Corzana, F. / Hurtado-Guerrero, R. | |||||||||
Citation | Journal: Nat.Commun. / Year: 2015 Title: Dynamic Interplay between Catalytic and Lectin Domains of Galnac-Transferases Modulates Protein O-Glycosylation. Authors: Lira-Navarrete, E. / De Las Rivas, M. / Companon, I. / Pallares, M.C. / Kong, Y. / Iglesias-Fernandez, J. / Bernardes, G.J.L. / Peregrina, J.M. / Rovira, C. / Bernado, P. / Bruscolini, P. / ...Authors: Lira-Navarrete, E. / De Las Rivas, M. / Companon, I. / Pallares, M.C. / Kong, Y. / Iglesias-Fernandez, J. / Bernardes, G.J.L. / Peregrina, J.M. / Rovira, C. / Bernado, P. / Bruscolini, P. / Clausen, H. / Lostao, A. / Corzana, 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 | 5ajp.cif.gz | 227.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ajp.ent.gz | 181.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ajp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ajp_validation.pdf.gz | 826.3 KB | Display | wwPDB validaton report |
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Full document | 5ajp_full_validation.pdf.gz | 829.1 KB | Display | |
Data in XML | 5ajp_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 5ajp_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/5ajp ftp://data.pdbj.org/pub/pdb/validation_reports/aj/5ajp | HTTPS FTP |
-Related structure data
Related structure data | 5ajnC 5ajoC 4d0tS C: citing same article (ref.) 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Protein/peptide / Sugars , 3 types, 3 molecules AB
#1: Protein | Mass: 64824.703 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): SMD1168 References: UniProt: Q10471, polypeptide N-acetylgalactosaminyltransferase |
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#2: Protein/peptide | Mass: 1546.632 Da / Num. of mol.: 1 / Fragment: RESIDUES 65-79 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): SMD1168 / References: UniProt: Q14886, UniProt: P98088*PLUS |
#6: Sugar | ChemComp-A2G / |
-Non-polymers , 4 types, 634 molecules
#3: Chemical | ChemComp-UDP / | ||||
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#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-MN / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.98 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. obs: 79709 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.9 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4D0T Resolution: 1.65→89.29 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.196 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.077 / 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: 28.104 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→89.29 Å
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Refine LS restraints |
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