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Open data
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Basic information
Entry | Database: PDB / ID: 8amh | ||||||
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Title | The Crystal structure of wt 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 | ![]() | 106.1 KB | Display | ![]() |
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PDB format | ![]() | 81.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.9 KB | Display | ![]() |
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Full document | ![]() | 452.3 KB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8an6C ![]() 8asrC ![]() 8assC ![]() 8astC ![]() 8asuC ![]() 8avjC ![]() 8avpC 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: Protein | Mass: 14806.284 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Agroavidin / 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: 1.98 Å3/Da / Density % sol: 37.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.1 M MgCl2, 0.1 M Bis-Tris pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→44.44 Å / Num. obs: 47014 / % possible obs: 99.5 % / Redundancy: 5.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.73→1.79 Å / Rmerge(I) obs: 1.09 / Num. unique obs: 4789 / CC1/2: 0.639 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: rhizavidin Resolution: 1.73→44.44 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.006 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.11 / 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: 28.28 Å2
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Refinement step | Cycle: 1 / Resolution: 1.73→44.44 Å
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Refine LS restraints |
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