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- PDB-4w81: Periplasmically Produced Monomeric Single Domain Antibody (sdAb) ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4w81 | ||||||
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Title | Periplasmically Produced Monomeric Single Domain Antibody (sdAb) C22A/C99V variant against Staphylococcal enterotoxin B (SEB) at pH 8.0 | ||||||
![]() | Single Domain Antibody | ||||||
![]() | IMMUNE SYSTEM / single domain antibody / v-set domain | ||||||
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 | ![]() | 40.5 KB | Display | ![]() |
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PDB format | ![]() | 26.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.4 KB | Display | ![]() |
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Full document | ![]() | 424.4 KB | Display | |
Data in XML | ![]() | 7.4 KB | Display | |
Data in CIF | ![]() | 9.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4tyuC ![]() 4u05C ![]() 4u7sC ![]() 4w68C ![]() 4w70SC 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
#1: Antibody | Mass: 15424.171 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#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 REFERENCE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.74 % / Description: Three-sided pyramid |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Hampton Ammonium Sulfate Grid Screen condition B5 0.1 M Tris pH 8.0, 1.6 M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: ![]() |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Aug 8, 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: 2.25→43.75 Å / Num. obs: 6314 / % possible obs: 99.5 % / Redundancy: 5.37 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.1301 / Rsym value: 0.1 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.25→2.35 Å / Redundancy: 3.46 % / Rmerge(I) obs: 0.4212 / Mean I/σ(I) obs: 3.19 / % possible all: 95.9 |
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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: 4W70 Resolution: 2.25→43.75 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.878 / SU B: 5.149 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.336 / ESU R Free: 0.223 / 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: 15.521 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→43.75 Å
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Refine LS restraints |
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