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Open data
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Basic information
Entry | Database: PDB / ID: 6and | ||||||
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Title | Pinatuzumab Fab in complex with anti-Kappa VHH domain | ||||||
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![]() | IMMUNE SYSTEM / Fab / antibody / CD22 / VHH domain | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ereno-Orbea, J. / Sicard, T. / Julien, J.-P. | ||||||
![]() | ![]() Title: Structural Basis of Enhanced Crystallizability Induced by a Molecular Chaperone for Antibody Antigen-Binding Fragments. Authors: Ereno-Orbea, J. / Sicard, T. / Cui, H. / Carson, J. / Hermans, P. / Julien, J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.3 KB | Display | ![]() |
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PDB format | ![]() | 91.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 303.3 KB | Display | ![]() |
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Full document | ![]() | 303.3 KB | Display | |
Data in XML | ![]() | 23.7 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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1 |
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Unit cell |
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Components
#1: Antibody | Mass: 10315.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() |
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#2: Antibody | Mass: 23833.525 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Antibody | Mass: 24062.736 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Sequence details | Anti-kappa VHH domain is represented as poly-UNK. The side chains were not included in the refinement. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M lithium sulfate, 0.1 M HEPES pH 7.4 and 25 % polyethyleneglycol (PEG) 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 10, 2016 | ||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||
Reflection | Resolution: 1.75→46.142 Å / Num. obs: 57457 / % possible obs: 93.6 % / Redundancy: 3.35 % / Biso Wilson estimate: 18.14 Å2 / Net I/σ(I): 16.05 | ||||||
Reflection shell |
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Processing
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Refinement | Resolution: 1.75→46.012 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→46.012 Å
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Refine LS restraints |
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LS refinement shell |
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