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Open data
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Basic information
Entry | Database: PDB / ID: 5lur | ||||||
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Title | An avidin mutant | ||||||
![]() | Avidin | ||||||
![]() | biotin binding protein / Avidin / antidins / steroids / progesterone / Steroid-binding | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Agrawal, N. / Lehtonen, S.I. / Riihimaki, T.A. / Kulomaa, M.S. / Hytonen, V.P. / Johnson, M.S. / Airenne, T.T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: An avidin mutant Authors: Agrawal, N. / Lehtonen, S.I. / Riihimaki, T.A. / Kulomaa, M.S. / Hytonen, V.P. / Johnson, M.S. / Airenne, T.T. | ||||||
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 KB | Display | ![]() |
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PDB format | ![]() | 45.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 707.4 KB | Display | ![]() |
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Full document | ![]() | 709.1 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4u46S 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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Symmetry | Point symmetry: (Schoenflies symbol: C2 (2 fold cyclic)) Helical symmetry: (Num. of operations: 2 / Rise per n subunits: 1 Å / Rotation per n subunits: 180 °) |
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Components
#1: Protein | Mass: 15863.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.23 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: Drop size: 150 nl of protein-ligand solution and well solution. Protein-ligand solution: 1.8 mg/ml of protein solution (20 mM sodium phosphate, 1M sodium chloride, 20mM imidazole, pH 7.4) ...Details: Drop size: 150 nl of protein-ligand solution and well solution. Protein-ligand solution: 1.8 mg/ml of protein solution (20 mM sodium phosphate, 1M sodium chloride, 20mM imidazole, pH 7.4) and 50 mM ligand solution (1.57 mg in 100 microL of water) were mixed in 10:1 (v/v) ratio. Well solution: 0.18 M sodium chloride, 0.09 M sodium cacodylate (pH 6.5) and 1.8 M ammonium sulfate. Temp details: Temperature-controlled incubator was used. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→19.56 Å / Num. obs: 7458 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.37 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.11 / CC1/2: 0.7 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4U46 Resolution: 2.7→19.56 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.895 / SU B: 13.075 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R Free: 0.349 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.703 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→19.56 Å
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Refine LS restraints |
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