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- PDB-8ass: The Crystal structure of F46Y mutant of the agroavidin-biotin complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ass | ||||||
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Title | The Crystal structure of F46Y mutant of the agroavidin-biotin complex | ||||||
![]() | Agroavidin | ||||||
![]() | UNKNOWN FUNCTION / BIOTIN BINDING PROTEIN / avidin / biotin / high affinity systems | ||||||
Function / homology | Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / biotin binding / extracellular region / BIOTIN / Avidin![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Livnah, O. / Bana, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Self-assembly of a dimeric avidin into unique higher-order oligomers. Authors: Bana, J. / Warwar, J. / Bayer, E.A. / Livnah, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.7 KB | Display | ![]() |
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PDB format | ![]() | 80.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 20.1 KB | Display | |
Data in CIF | ![]() | 26.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8amhC ![]() 8an6SC ![]() 8asrC ![]() 8astC ![]() 8asuC ![]() 8avjC ![]() 8avpC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14822.284 Da / Num. of mol.: 4 / Mutation: F46Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-BTN / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis Tris pH 5.8 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→43.8 Å / Num. obs: 24821 / % possible obs: 95.5 % / Redundancy: 4.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.109 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.12→2.19 Å / Rmerge(I) obs: 0.977 / Num. unique obs: 2348 / CC1/2: 0.492 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8AN6 Resolution: 2.12→43.8 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.864 / SU B: 12.543 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R: 0.367 / ESU R Free: 0.289 / 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: 43.528 Å2
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Refinement step | Cycle: 1 / Resolution: 2.12→43.8 Å
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Refine LS restraints |
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