+Open data
-Basic information
Entry | Database: PDB / ID: 5a2i | |||||||||
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Title | Crystal structure of scFv-SM3 in complex with APD-SGalNAc-RP | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / GLYCOPEPTIDES / ANTIBODIES / MOLECULAR RECOGNITION / CONFORMATION ANALYSIS / FUSION PROTEIN | |||||||||
Function / homology | Function and homology information immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / adaptive immune response / blood microparticle / immune response / extracellular space Similarity search - Function | |||||||||
Biological species | MUS MUSCULUS (house mouse) HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | |||||||||
Authors | Martinez-Saez, N. / Castro-Lopez, J. / Valero-Gonzalez, J. / Madariaga, D. / Companon, I. / Somovilla, V.J. / Salvado, M. / Asensio, J.L. / Jimenez-Barbero, J. / Avenoza, A. ...Martinez-Saez, N. / Castro-Lopez, J. / Valero-Gonzalez, J. / Madariaga, D. / Companon, I. / Somovilla, V.J. / Salvado, M. / Asensio, J.L. / Jimenez-Barbero, J. / Avenoza, A. / Busto, J.H. / Bernardes, G.J.L. / Peregrina, J.M. / Hurtado-Guerrero, R. / Corzana, F. | |||||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: Deciphering the Non-Equivalence of Serine and Threonine O-Glycosylation Points: Implications for Molecular Recognition of the Tn Antigen by an Anti-Muc1 Antibody. Authors: Martinez-Saez, N. / Castro-Lopez, J. / Valero-Gonzalez, J. / Madariaga, D. / Companon, I. / Somovilla, V.J. / Salvado, M. / Asensio, J.L. / Jimenez-Barbero, J. / Avenoza, A. / Busto, J.H. / ...Authors: Martinez-Saez, N. / Castro-Lopez, J. / Valero-Gonzalez, J. / Madariaga, D. / Companon, I. / Somovilla, V.J. / Salvado, M. / Asensio, J.L. / Jimenez-Barbero, J. / Avenoza, A. / Busto, J.H. / Bernardes, G.J.L. / Peregrina, J.M. / Hurtado-Guerrero, R. / Corzana, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a2i.cif.gz | 102.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a2i.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 5a2i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a2i_validation.pdf.gz | 472.2 KB | Display | wwPDB validaton report |
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Full document | 5a2i_full_validation.pdf.gz | 475.9 KB | Display | |
Data in XML | 5a2i_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 5a2i_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/5a2i ftp://data.pdbj.org/pub/pdb/validation_reports/a2/5a2i | HTTPS FTP |
-Related structure data
Related structure data | 5a2jC 5a2kC 5a2lC 1sm3S 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
#1: Antibody | Mass: 25742.338 Da / Num. of mol.: 1 / Fragment: RESIDUES 6-115,20-129 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PPICZALPHAA / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): X33 / References: UniProt: P01801, UniProt: P01727 | ||||||
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#2: Protein/peptide | Mass: 642.682 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) | ||||||
#3: Chemical | #4: Sugar | ChemComp-A2G / | #5: Water | ChemComp-HOH / | Sequence details | RESIDUE RANGE 1002-1107 FOR CHAIN H MAPS TO CHAIN L OF PDB ENTRY 1SM3. CHAIN P REPRESENTS A SHORTER ...RESIDUE RANGE 1002-1107 FOR CHAIN H MAPS TO CHAIN L OF PDB ENTRY 1SM3. CHAIN P REPRESENTS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.31 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→20 Å / Num. obs: 16818 / % possible obs: 99.9 % / Observed criterion σ(I): 1.8 / Redundancy: 6.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.88→1.98 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SM3 Resolution: 1.88→90.29 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 11.873 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.168 / 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: 36.065 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→90.29 Å
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Refine LS restraints |
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