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Open data
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Basic information
Entry | Database: PDB / ID: 8bl6 | |||||||||
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Title | De novo single-chain immunoglobulin dimer scIg12+EF3a | |||||||||
![]() | dIG14-scdim-EF62 | |||||||||
![]() | DE NOVO PROTEIN / de novo / immunoglobulin / single-chain dimer / sandwich / beta / EF-hand | |||||||||
Function / homology | TERBIUM(III) ION![]() | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nadal, M. / Roel-Touris, J. / Marcos, E. | |||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: Single-chain dimers from de novo immunoglobulins as robust scaffolds for multiple binding loops. Authors: Roel-Touris, J. / Nadal, M. / Marcos, E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.9 KB | Display | ![]() |
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PDB format | ![]() | 28.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.1 KB | Display | ![]() |
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Full document | ![]() | 441.8 KB | Display | |
Data in XML | ![]() | 7.4 KB | Display | |
Data in CIF | ![]() | 8.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bl3C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20141.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
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#2: Chemical | ChemComp-GOL / | ||
#3: Chemical | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.07 Å3/Da / Density % sol: 69.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG MME 2000 20.0%w/v, TRIS 0.1M pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2022 |
Radiation | Monochromator: 1.50102 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.50102 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→58.59 Å / Num. obs: 7030 / % possible obs: 100 % / Redundancy: 16.2 % / CC1/2: 0.944 / Rmerge(I) obs: 0.016 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.8→2.95 Å / Num. unique obs: 1001 / CC1/2: 0.876 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Model prediction Resolution: 2.8→58.59 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.006 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.483 / ESU R Free: 0.319 / 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: 94.072 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→58.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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