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Open data
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Basic information
Entry | Database: PDB / ID: 4z6j | ||||||
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Title | Crystal structure of apo intact hoefavidin | ||||||
![]() | Avidin family | ||||||
![]() | Biotin-binding protein / high affinity system / bacterial avidins | ||||||
Function / homology | ![]() biotin binding / protein homodimerization activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Livnah, O. / Avraham, O. | ||||||
![]() | ![]() Title: Hoefavidin: A dimeric bacterial avidin with a C-terminal binding tail. Authors: Avraham, O. / Meir, A. / Fish, A. / 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 | ![]() | 114.3 KB | Display | ![]() |
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PDB format | ![]() | 90 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4z27C ![]() 4z28C ![]() 4z2oC ![]() 4z2pC ![]() 4z2vC ![]() 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 17 - 144 / Label seq-ID: 17 - 144
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Components
#1: Protein | Mass: 15372.627 Da / Num. of mol.: 2 / Fragment: UNP residues 21-165 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: HPDFL43_17171 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.5-1.8 M Li2SO4 and 0.1 M HEPES (pH 7.5-7.7) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 10687 / % possible obs: 99.6 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 38 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.227 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ew1 Resolution: 2.4→47.97 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.899 / SU B: 21.37 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R: 0.64 / ESU R Free: 0.323 / 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: 48.032 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→47.97 Å
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Refine LS restraints |
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