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Open data
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Basic information
Entry | Database: PDB / ID: 4ggr | ||||||
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Title | The structure of apo bradavidin2 (Form A) | ||||||
![]() | Bradavidin 2 | ||||||
![]() | BIOTIN BINDING PROTEIN / bradavidin / avidin / oligomeric state / streptavidin / high affinity systems / lipocalin fold / beta barrel | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Livnah, O. / Meir, A. | ||||||
![]() | ![]() Title: The highly dynamic oligomeric structure of bradavidin II is unique among avidin proteins. Authors: Leppiniemi, J. / Meir, A. / Kahkonen, N. / Kukkurainen, S. / Maatta, J.A. / Ojanen, M. / Janis, J. / Kulomaa, M.S. / Livnah, O. / 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 | ![]() | 34.3 KB | Display | ![]() |
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PDB format | ![]() | 22.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419.2 KB | Display | ![]() |
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Full document | ![]() | 421.2 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 8.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ggtC ![]() 4ggzC ![]() 3ew1S C: citing same article ( 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 12581.157 Da / Num. of mol.: 1 / Fragment: UNP residues 19-130 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.01 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 8.5 Details: 30% PEG4000, 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, MICROBATCH, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 2, 2010 |
Radiation | Monochromator: Diamond(001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 9133 / Num. obs: 9133 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3EW1 Resolution: 1.9→42.17 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.163 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.17 / 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: 35.469 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→42.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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