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Yorodumi- PDB-4z0b: Crystal Structure of the Fab Fragment of Anti-ofloxacin Antibody ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z0b | ||||||
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Title | Crystal Structure of the Fab Fragment of Anti-ofloxacin Antibody and Exploration Its Receptor Binding Site | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Ofloxacin ELISA Fab | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | He, K. / Du, X. / Sheng, W. / Zhou, X. / Wang, J. / Wang, S. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Agric.Food Chem. / Year: 2016 Title: Crystal Structure of the Fab Fragment of an Anti-ofloxacin Antibody and Exploration of Its Specific Binding. Authors: He, K. / Du, X. / Sheng, W. / Zhou, X. / Wang, J. / Wang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z0b.cif.gz | 92.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z0b.ent.gz | 68.6 KB | Display | PDB format |
PDBx/mmJSON format | 4z0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/4z0b ftp://data.pdbj.org/pub/pdb/validation_reports/z0/4z0b | HTTPS FTP |
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-Related structure data
Related structure data | 1ar1S 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: 23826.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 |
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#2: Antibody | Mass: 22725.779 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 |
#3: Chemical | ChemComp-PO4 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.85 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / Details: 0.2M ammonium phosphate dibasic, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 7100 / % possible obs: 90 % / Redundancy: 2.9 % / Net I/σ(I): 9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AR1 Resolution: 3.2→50 Å / Cor.coef. Fo:Fc: 0.84 / Cor.coef. Fo:Fc free: 0.806 / SU B: 37.959 / SU ML: 0.608 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.774 / 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 max: 93.5 Å2 / Biso mean: 55.508 Å2 / Biso min: 35.24 Å2
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Refinement step | Cycle: final / Resolution: 3.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.283 Å / Total num. of bins used: 20
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