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Open data
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Basic information
Entry | Database: PDB / ID: 8g0i | ||||||
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Title | High Affinity nanobodies against GFP | ||||||
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![]() | IMMUNE SYSTEM / Nanobody / nanobodies / GFP / green fluorescent protein / high-affinity antibody variant / antibody variant / single-domain antibody | ||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein![]() | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ketaren, N.E. / Rout, M.P. / Almo, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: High Affinity nanobodies against GFP Authors: Ketaren, N.E. / Rout, M.P. / Almo, 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 | ![]() | 204.7 KB | Display | ![]() |
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PDB format | ![]() | 165.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.4 KB | Display | ![]() |
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Full document | ![]() | 449.2 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sfsC ![]() 8sfxC ![]() 8sfzC ![]() 8sg3C ![]() 8slcC 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 on special symmetry positions |
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Components
#1: Protein | Mass: 28794.396 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Antibody | Mass: 14780.458 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.16 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium chloride, 20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0705 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 19251 / % possible obs: 99.5 % / Redundancy: 10 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Χ2: 1.529 / Net I/av σ(I): 33.886 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 7 / Num. unique obs: 864 / Rsym value: 0.726 / Χ2: 0.835 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 2.2→44.65 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 18.0606 Å / Origin y: 93.5342 Å / Origin z: 62.2825 Å
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Refinement TLS group | Selection details: all |