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Open data
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Basic information
Entry | Database: PDB / ID: 8asr | ||||||
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Title | The Crystal structure of F46Y mutant of apo agroavidin | ||||||
![]() | 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 | ![]() | 113.6 KB | Display | ![]() |
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PDB format | ![]() | 87.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448 KB | Display | ![]() |
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Full document | ![]() | 452.4 KB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 33.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8amhC ![]() 8an6C ![]() 8assC ![]() 8astC ![]() 8asuC ![]() 8avjC ![]() 8avpC ![]() 3ew1S 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: 14822.284 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: 2.02 Å3/Da / Density % sol: 39.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 18% pentaerythritol ethoxylate, 0.05 M Bis Tris pH 5.9-6.0, 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: Feb 2, 2018 / Details: optical hatch |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→44.76 Å / Num. obs: 53732 / % possible obs: 98.6 % / Redundancy: 4.3 % / CC1/2: 0.99 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.66→1.72 Å / Rmerge(I) obs: 0.778 / Num. unique obs: 5477 / CC1/2: 0.794 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ew1 Resolution: 1.66→44.76 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.261 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.101 / 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: 24.271 Å2
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Refinement step | Cycle: 1 / Resolution: 1.66→44.76 Å
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Refine LS restraints |
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