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Open data
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Basic information
Entry | Database: PDB / ID: 4u46 | ||||||
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Title | Crystal structure of an avidin mutant | ||||||
![]() | Avidin | ||||||
![]() | Biotin binding protein / Avidin / Biotin / Ligand binding / Sterols | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Agrawal, N. / Lehtonen, S. / Kahkonen, N. / Riihimaki, T. / Hytonen, V.P. / Kulomaa, M.S. / Johnson, M.S. / Airenne, T.T. | ||||||
![]() | ![]() Title: Artificial Avidin-Based Receptors for a Panel of Small Molecules. Authors: Lehtonen, S.I. / Tullila, A. / Agrawal, N. / Kukkurainen, S. / Kahkonen, N. / Koskinen, M. / Nevanen, T.K. / Johnson, M.S. / Airenne, T.T. / Kulomaa, M.S. / Riihimaki, T.A. / Hytonen, V.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.2 KB | Display | ![]() |
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PDB format | ![]() | 45.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 350 KB | Display | ![]() |
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Full document | ![]() | 350.3 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 9.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wbiS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 15863.781 Da / Num. of mol.: 2 / Fragment: UNP residues 25-152 Source method: isolated from a genetically manipulated source Details: OmpA signal was used in expression. / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: 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: 39.02 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: Well solution: 0.2 M sodium chloride, 0.1 M sodium cacodylate, 2.0 M ammonium sulphate PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→25 Å / Num. all: 19367 / Num. obs: 19264 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 5 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WBI Resolution: 1.95→19.34 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.038 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.139 / 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: 32.228 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→19.34 Å
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Refine LS restraints |
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