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Open data
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Basic information
Entry | Database: PDB / ID: 4ggt | ||||||
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Title | Structure of apo Bradavidin2 (Form B) | ||||||
![]() | 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 | ![]() | 57.3 KB | Display | ![]() |
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PDB format | ![]() | 41.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.2 KB | Display | ![]() |
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Full document | ![]() | 448.3 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ggrC ![]() 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12581.157 Da / Num. of mol.: 2 / Fragment: UNP residues 19-130 Source method: isolated from a genetically manipulated source 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: 2.48 Å3/Da / Density % sol: 50.4 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 3 Details: 1 uL drop of 3.4 mg/mL protein in 0.5 M acetic acid, pH 3.0, with 0.12 M magnesium formate, diffraction parameters improved with later addition of 0.1 M sodium bromide, MICROBATCH, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2011 |
Radiation | Monochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.693→50 Å / Num. all: 23010 / Num. obs: 23010 / % possible obs: 86 % / 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: 1.693→40.66 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.34 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.135 / 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: 26.69 Å2
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Refinement step | Cycle: LAST / Resolution: 1.693→40.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.693→1.737 Å / Total num. of bins used: 20
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