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- PDB-9luy: Single-chain Fv antibody of G2 fused with antigen peptide from ch... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9luy | ||||||
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Title | Single-chain Fv antibody of G2 fused with antigen peptide from chicken chromosome 6 C10orf76 homolog | ||||||
![]() | Single-chain Fv antibody of G2 fused with antigen peptide from chicken chromosome 6 C10orf76 homolog | ||||||
![]() | IMMUNE SYSTEM / ANTIGEN BINDING / AFFINITY MATURATION / SOMATIC HYPERMUTATION | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hanazono, Y. / Yabuno, S. / Hayashi, T. / Numoto, N. / Ito, N. / Oda, M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structures reveal how the multispecific antibody G2 achieves binding to different peptides. Authors: Hanazono, Y. / Yabuno, S. / Hayashi, T. / Numoto, N. / Kamatari, Y.O. / Ito, N. / Oda, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127 KB | Display | ![]() |
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PDB format | ![]() | 85.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.9 KB | Display | ![]() |
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Full document | ![]() | 431.9 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 20.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Antibody | Mass: 29120.334 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The fusion protein composed of an expression tag (residues 1-2), a fragment from chicken chromosome 6 C10orf76 homolog (residues 3-22), a linker (residues 23-30), the light chain (residues ...Details: The fusion protein composed of an expression tag (residues 1-2), a fragment from chicken chromosome 6 C10orf76 homolog (residues 3-22), a linker (residues 23-30), the light chain (residues 31-140), a second linker (residues 141-155), and the heavy chain (residues 156-273). Source: (gene. exp.) ![]() ![]() ![]() ![]() Production host: ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES monohydrate pH 6.5, 12% w/v polyethylene glycol 20,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 17, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→50 Å / Num. obs: 28848 / % possible obs: 99.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.29 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.62→1.65 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.712 / Mean I/σ(I) obs: 2 / Num. unique obs: 1429 / CC1/2: 0.656 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6PGX Resolution: 1.62→31.14 Å / SU ML: 0.1567 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8971 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→31.14 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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