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- PDB-5n7b: Understanding the singular conformational landscape of the Tn ant... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5n7b | |||||||||
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Title | Understanding the singular conformational landscape of the Tn antigens: Sulfur-for- oxygen substitution in the glycosidic linkage provides new insights into molecular recognition by an antibody | |||||||||
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![]() | IMMUNE SYSTEM / ANTIBODIES / ANTIGEN Tn | |||||||||
Function / homology | ![]() immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / adaptive immune response / blood microparticle / immune response / extracellular space Similarity search - Function | |||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Companon, I. / Martinez-Saez, N. / Castro-Lopez, J. / Jimenez-Barbero, J. / Bernardes, G.J.L. / Busto, J.H. / Avenoza, A. / Jimenez-Oses, G. / Hurtado-Guerrero, R. / Peregrina, J.M. / Corzana, F. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Based Design of Potent Tumor-Associated Antigens: Modulation of Peptide Presentation by Single-Atom O/S or O/Se Substitutions at the Glycosidic Linkage. Authors: Companon, I. / Guerreiro, A. / Mangini, V. / Castro-Lopez, J. / Escudero-Casao, M. / Avenoza, A. / Busto, J.H. / Castillon, S. / Jimenez-Barbero, J. / Asensio, J.L. / Jimenez-Oses, G. / ...Authors: Companon, I. / Guerreiro, A. / Mangini, V. / Castro-Lopez, J. / Escudero-Casao, M. / Avenoza, A. / Busto, J.H. / Castillon, S. / Jimenez-Barbero, J. / Asensio, J.L. / Jimenez-Oses, G. / Boutureira, O. / Peregrina, J.M. / Hurtado-Guerrero, R. / Fiammengo, R. / Bernardes, G.J.L. / Corzana, F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.3 KB | Display | ![]() |
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PDB format | ![]() | 48.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.6 KB | Display | ![]() |
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Full document | ![]() | 481.7 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 19.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6frjC ![]() 5a2iS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 25758.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Please follow the numbering described in the PDB entry 5A2K Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein/peptide | Mass: 670.782 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
#3: Chemical | ChemComp-EDO / #4: Sugar | ChemComp-A2G / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.15 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M disodium hydrogen phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 25141 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rpim(I) all: 0.035 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.4 / CC1/2: 0.867 / Rpim(I) all: 0.317 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5A2I Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.411 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.106 / 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: 24.071 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→20 Å
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Refine LS restraints |
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