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Open data
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Basic information
Entry | Database: PDB / ID: 8ast | ||||||
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Title | The Crystal structure of short F46Y agroavidin - apo | ||||||
![]() | 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 / 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 | ![]() | 102.3 KB | Display | ![]() |
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PDB format | ![]() | 77.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8amhC ![]() 8an6C ![]() 8asrSC ![]() 8assC ![]() 8asuC ![]() 8avjC ![]() 8avpC C: citing same article ( S: Starting model for refinement |
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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: Protein | Mass: 13794.177 Da / Num. of mol.: 4 / Mutation: F46Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 18% pentaerythritol ethoxylate, 0.05 M Bis Tris pH 6.0, 0.05 M ammonium sulphate |
-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: Nov 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→52.56 Å / Num. obs: 66081 / % possible obs: 94.7 % / Redundancy: 4.7 % / CC1/2: 0.993 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.55→1.59 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4765 / CC1/2: 0.469 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8ASR Resolution: 1.55→52.55 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.194 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.092 / 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: 24.433 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→52.55 Å
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Refine LS restraints |
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