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- PDB-4w68: Cytoplasmically Produced Homodimeric Single Domain Antibody (sdAb... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4w68 | ||||||
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Title | Cytoplasmically Produced Homodimeric Single Domain Antibody (sdAb) C22A/C99V variant against Staphylococcal enterotoxin B (SEB) | ||||||
![]() | Single domain antibody | ||||||
![]() | IMMUNE SYSTEM / beta helical / amyloid-like / misfolded / dimeric | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | George, J. / Legler, P.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and mutational analysis of a monomeric and dimeric form of a single domain antibody with implications for protein misfolding. Authors: George, J. / Compton, J.R. / Leary, D.H. / Olson, M.A. / Legler, P.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.2 KB | Display | ![]() |
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PDB format | ![]() | 45.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.9 KB | Display | ![]() |
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Full document | ![]() | 427.4 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 16.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4tyuSC ![]() 4u05C ![]() 4u7sC ![]() 4w70C ![]() 4w81C S: Starting model for refinement C: citing same article ( |
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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
#1: Antibody | Mass: 14350.981 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | Compound details | SEQUENCE REFLECTS C22A, C99V MUTATIONS AGAINST WT PROTEIN. NO UNP MATCH IS FOUND, THEREFORE THE ...SEQUENCE REFLECTS C22A, C99V MUTATIONS AGAINST WT PROTEIN. NO UNP MATCH IS FOUND, THEREFORE THE SEQUENCE IS SELF REFERENCED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.47 % / Description: rod-shaped |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Tris pH 8.0, 1.6 M Ammonium Sulfate [Hampton Research Ammonium Sulfate Grid Screen, condition B5] |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: ![]() |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Sep 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→58.05 Å / Num. obs: 18197 / % possible obs: 94.3 % / Redundancy: 10.57 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.1038 / Rsym value: 0.054 / Net I/σ(I): 16.86 |
Reflection shell | Resolution: 2→2.09 Å / Redundancy: 2.29 % / Rmerge(I) obs: 0.3556 / Mean I/σ(I) obs: 3.32 / % possible all: 71.8 |
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Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 4TYU Resolution: 2→58.05 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.892 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 14.252 Å2
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Refinement step | Cycle: 1 / Resolution: 2→58.05 Å
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Refine LS restraints |
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