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Yorodumi- PDB-5a2j: Crystal structure of scFv-SM3 in complex with the naked peptide APDTRP -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a2j | ||||||
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Title | Crystal structure of scFv-SM3 in complex with the naked peptide APDTRP | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / 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: 1.65 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 | 5a2j.cif.gz | 104.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a2j.ent.gz | 79.5 KB | Display | PDB format |
PDBx/mmJSON format | 5a2j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a2j_validation.pdf.gz | 456.1 KB | Display | wwPDB validaton report |
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Full document | 5a2j_full_validation.pdf.gz | 458.7 KB | Display | |
Data in XML | 5a2j_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 5a2j_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/5a2j ftp://data.pdbj.org/pub/pdb/validation_reports/a2/5a2j | HTTPS FTP |
-Related structure data
Related structure data | 5a2iC 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 Details: CONTAINS BOTH H AND L CHAINS OF SCFV-SM3, CONNECTEDBY A LINKER. CHAIN L RESIDUES ARE NUMBERED FROM 1000. Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PPICZALPHAA / Production host: KOMAGATAELLA PASTORIS (fungus) / References: UniProt: P01801, UniProt: P01727 | ||||
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#2: Protein/peptide | Mass: 656.708 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) | ||||
#3: Chemical | ChemComp-EDO / #4: 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: 2.11 Å3/Da / Density % sol: 41.84 % / 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 / 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: 1.65→20 Å / Num. obs: 26087 / % possible obs: 97.1 % / Observed criterion σ(I): 1.98 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SM3 Resolution: 1.65→68.66 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.23 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.094 / 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: 14.762 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→68.66 Å
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Refine LS restraints |
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