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Open data
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Basic information
Entry | Database: PDB / ID: 8be3 | ||||||
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Title | Crystal structure of KRasG12V-Nanobody84 | ||||||
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![]() | SIGNALING PROTEIN / Complex / Stabilizer | ||||||
Function / homology | small monomeric GTPase / Ca2+ pathway / GUANOSINE-5'-DIPHOSPHATE / Isoform 2B of GTPase KRas![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fischer, B. / Wohlkonig, A. / Steyaert, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Allosteric nanobodies to study the interactions between SOS1 and RAS. Authors: Fischer, B. / Uchanski, T. / Sheryazdanova, A. / Gonzalez, S. / Volkov, A.N. / Brosens, E. / Zogg, T. / Kalichuk, V. / Ballet, S. / Versees, W. / Sablina, A.A. / Pardon, E. / Wohlkonig, A. / Steyaert, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136.1 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 24.6 KB | Display | |
Data in CIF | ![]() | 35.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8be2C ![]() 8be4C ![]() 8be5C ![]() 4l9sS S: Starting model for refinement 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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2 |
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Unit cell |
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Components
#1: Antibody | Mass: 13519.057 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 21675.314 Da / Num. of mol.: 2 / Mutation: G12V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350 21%, MES 0.1 M pH 6.0, NaCl 150mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→42.3 Å / Num. obs: 54015 / % possible obs: 98.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 33.43 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.85→1.96 Å / Num. unique obs: 38376 / CC1/2: 0.66 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4L9S Resolution: 1.85→42.3 Å / SU ML: 0.232 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.8998 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: 41.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→42.3 Å
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Refine LS restraints |
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LS refinement shell |
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