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- PDB-8avp: Structure of short biotin complexed agroavidin with the Hoef tail. -
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Open data
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Basic information
Entry | Database: PDB / ID: 8avp | ||||||
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Title | Structure of short biotin complexed agroavidin with the Hoef tail. | ||||||
![]() | agroavCH | ||||||
![]() | UNKNOWN FUNCTION / avidin / streptavidin / high-affinity systems / dimeric avidins / multimers | ||||||
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. / Warar, 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 | ![]() | 452 KB | Display | ![]() |
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PDB format | ![]() | 372.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8amhC ![]() 8an6C ![]() 8asrC ![]() 8assC ![]() 8astSC ![]() 8asuC ![]() 8avjC 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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Unit cell |
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Components
#1: Protein | Mass: 13751.172 Da / Num. of mol.: 20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-BTN / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% ethylene glycol 0.05M acetic acid pH 3.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965 Å / Relative weight: 1 |
Reflection | Resolution: 2.87→50 Å / Num. obs: 74109 / % possible obs: 99.3 % / Redundancy: 3.35 % / CC1/2: 0.993 / Rmerge(I) obs: 0.089 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.87→2.96 Å / Rmerge(I) obs: 0.932 / Num. unique obs: 4436 / CC1/2: 0.465 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8AST Resolution: 2.87→50 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.868 / SU B: 21.557 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / 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 |
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Refinement step | Cycle: 1 / Resolution: 2.87→50 Å
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Refine LS restraints |
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