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Open data
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Basic information
Entry | Database: PDB / ID: 8sfx | ||||||
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Title | High Affinity nanobodies against GFP | ||||||
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![]() | ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ketaren, N.E. / Rout, M.P. / Bonanno, J.B. / Almo, S.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: High Affinity nanobodies against GFP Authors: Ketaren, N.E. / Bonanno, J.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 411.1 KB | Display | ![]() |
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PDB format | ![]() | 340.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8g0iC ![]() 8sfsC ![]() 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
-Protein , 2 types, 4 molecules ABDC
#1: Protein | ![]() Mass: 28794.396 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein | Mass: 15470.181 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 179 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/MLT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MLT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GOL / ![]() #4: Chemical | ![]() #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-PO4 / ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.67 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 1 M bis-tris propane pH 7.0, 1.2 M DL-malic acid pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.95→100 Å / Num. obs: 85311 / % possible obs: 100 % / Redundancy: 15.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.95→2.06 Å / Rmerge(I) obs: 1.403 / Mean I/σ(I) obs: 2 / Num. unique obs: 12451 / % possible all: 100 |
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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: 1.95→36.67 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: -27.8072 Å / Origin y: -10.3191 Å / Origin z: 5.773 Å
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Refinement TLS group | Selection details: all |