+Open data
-Basic information
Entry | Database: PDB / ID: 5fxc | ||||||
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Title | Crystal structure of glycopeptide 22 in complex with scFv-SM3 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / GLYCOPEPTIDES / ANTIBODIES / MOLECULAR RECOGNITION / CONFORMATION ANALYSIS | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Rojas-Ocariz, V. / Companon, I. / Aydillo, C. / Castro-Lopez, J. / Jimenez-Barbero, J. / Hurtado-Guerrero, R. / Avenoza, A. / Zurbano, M.M. / Corzana, F. / Busto, J.H. / Peregrina, J.M. | ||||||
Citation | Journal: J.Org.Chem. / Year: 2016 Title: Design of Alpha-S-Glycopeptides Derived from Muc1 with a Flexible and Solvent Exposed Sugar Moiety Authors: Rojas-Ocariz, V. / Companon, I. / Aydillo, C. / Castro-Lopez, J. / Jimenez-Barbero, J. / Hurtado-Guerrero, R. / Avenoza, A. / Zurbano, M.M. / Corzana, F. / Busto, J.H. / Peregrina, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fxc.cif.gz | 102.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fxc.ent.gz | 78.1 KB | Display | PDB format |
PDBx/mmJSON format | 5fxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fxc_validation.pdf.gz | 448.1 KB | Display | wwPDB validaton report |
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Full document | 5fxc_full_validation.pdf.gz | 452.5 KB | Display | |
Data in XML | 5fxc_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 5fxc_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/5fxc ftp://data.pdbj.org/pub/pdb/validation_reports/fx/5fxc | HTTPS FTP |
-Related structure data
Related structure data | 5a2iS 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: 25758.338 Da / Num. of mol.: 1 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 | ||
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#2: Protein/peptide | Mass: 656.708 Da / Num. of mol.: 1 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 | ||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.4 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97 |
Detector | Type: DECTRIS PILATUS 6M / 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: 2.05→20 Å / Num. obs: 14126 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 5 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.1 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5A2I Resolution: 2.05→54.38 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.918 / SU B: 13.541 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.213 / 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: 37.924 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→54.38 Å
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Refine LS restraints |
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