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Yorodumi- PDB-4d11: GalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 peptide and mang... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d11 | ||||||
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Title | GalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 peptide and manganese (Lower resolution dataset) | ||||||
Components |
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Keywords | TRANSFERASE/PEPTIDE / TRANSFERASE-PEPTIDE COMPLEX / RETAINING GALNAC-T2 / SUBSTRATE-GUIDED SNI-TYPE REACTION / QM/MM METADYNAMICS / BI-BI KINETIC MECHANISM / SUBSTRATE SPECIFICITY / ACETAMIDO GROUP | ||||||
Function / homology | Function and homology information intussusceptive angiogenesis / apoptotic process involved in heart morphogenesis / chorio-allantoic fusion / protein O-linked glycosylation via threonine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via serine / chondroblast differentiation / positive regulation of ceramide biosynthetic process / O-glycan processing ...intussusceptive angiogenesis / apoptotic process involved in heart morphogenesis / chorio-allantoic fusion / protein O-linked glycosylation via threonine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via serine / chondroblast differentiation / positive regulation of ceramide biosynthetic process / O-glycan processing / atrial septum morphogenesis / positive regulation of cartilage development / O-linked glycosylation of mucins / Golgi stack / COPI-independent Golgi-to-ER retrograde traffic / protein O-linked glycosylation / extracellular matrix binding / positive regulation of cell-substrate adhesion / atrioventricular valve morphogenesis / labyrinthine layer blood vessel development / ventricular septum development / Golgi cisterna membrane / protein maturation / reactive oxygen species metabolic process / extracellular matrix organization / positive regulation of cell differentiation / osteoblast differentiation / integrin binding / manganese ion binding / carbohydrate binding / positive regulation of cell migration / positive regulation of apoptotic process / Golgi membrane / nucleotide binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / extracellular region / membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Lira-Navarrete, E. / Iglesias-Fernandez, J. / Zandberg, W.F. / Companon, I. / Kong, Y. / Corzana, F. / Pinto, B.M. / Clausen, H. / Peregrina, J.M. / Vocadlo, D. ...Lira-Navarrete, E. / Iglesias-Fernandez, J. / Zandberg, W.F. / Companon, I. / Kong, Y. / Corzana, F. / Pinto, B.M. / Clausen, H. / Peregrina, J.M. / Vocadlo, D. / Rovira, C. / Hurtado-Guerrero, R. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 Title: Substrate-Guided Front-Face Reaction Revealed by Combined Structural Snapshots and Metadynamics for the Polypeptide N- Acetylgalactosaminyltransferase 2. Authors: Lira-Navarrete, E. / Iglesias-Fernandez, J. / Zandberg, W.F. / Companon, I. / Kong, Y. / Corzana, F. / Pinto, B.M. / Clausen, H. / Peregrina, J.M. / Vocadlo, D. / Rovira, C. / 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 | 4d11.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4d11.ent.gz | 900 KB | Display | PDB format |
PDBx/mmJSON format | 4d11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/4d11 ftp://data.pdbj.org/pub/pdb/validation_reports/d1/4d11 | HTTPS FTP |
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-Related structure data
Related structure data | 4d0tC 4d0zC 2ffvS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper: (Code: given Matrix: (-0.08242, -0.02447, 0.9963), Vector: |
-Components
-POLYPEPTIDE GALNAC-TRANSFERASE ... , 2 types, 6 molecules ABDEFC
#1: Protein | Mass: 64824.703 Da / Num. of mol.: 5 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): SMD-1168 / References: UniProt: Q10471 #2: Protein | | Mass: 64854.727 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): SMD-1168 / References: UniProt: Q10471 |
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-Protein/peptide / Sugars , 2 types, 9 molecules LOPXZ
#3: Protein/peptide | Mass: 548.610 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): SMD-1168 / References: UniProt: Q6FI18*PLUS #5: Sugar | ChemComp-BBK / |
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-Non-polymers , 2 types, 12 molecules
#4: Chemical | ChemComp-MN / #6: Chemical | ChemComp-UDP / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.31 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.96 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→47 Å / Num. obs: 83233 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.85→3 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FFV Resolution: 2.85→249.61 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.914 / SU B: 33.179 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R Free: 0.352 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.266 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→249.61 Å
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Refine LS restraints |
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