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- PDB-5i76: Crystal structure of FM318, a recombinant Fab adopted from cetuximab -
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Open data
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Basic information
Entry | Database: PDB / ID: 5i76 | ||||||
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Title | Crystal structure of FM318, a recombinant Fab adopted from cetuximab | ||||||
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Function / homology | ![]() ![]() ![]() ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sim, D.W. / Kim, J.H. / Seok, S.H. / Seo, M.D. / Kim, Y.P. / Won, H.S. | ||||||
![]() | ![]() Title: Bacterial production and structure-functional validation of a recombinant antigen-binding fragment (Fab) of an anti-cancer therapeutic antibody targeting epidermal growth factor receptor. Authors: Kim, J.H. / Sim, D.W. / Park, D. / Jung, T.G. / Lee, S. / Oh, T. / Ha, J.R. / Seok, S.H. / Seo, M.D. / Kang, H.C. / Kim, Y.P. / Won, H.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 334.1 KB | Display | ![]() |
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PDB format | ![]() | 272.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1yy8S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23519.963 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() ![]() #2: Antibody | Mass: 24072.916 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.34 % |
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Crystal grow![]() | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% (w/v) PEG 3000 100 mM Imidazole/ Hydrochloric acid pH 8.0 200 mM Zinc acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 30, 2014 |
Radiation | Monochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.92→27.72 Å / Num. obs: 69631 / % possible obs: 98.4 % / Redundancy: 7.5 % / Biso Wilson estimate: 21.03 Å2 / Rsym value: 0.076 / Net I/σ(I): 45.25 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 11.26 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1YY8 Resolution: 1.922→27.717 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.16
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.922→27.717 Å
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Refine LS restraints |
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LS refinement shell |
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