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Yorodumi- PDB-4u05: Homodimeric Single Domain Antibody (sdAb) against Staphylococcal ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u05 | ||||||
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Title | Homodimeric Single Domain Antibody (sdAb) against Staphylococcal enterotoxin B (SEB) S74A Variant | ||||||
Components | Single Domain Antibody | ||||||
Keywords | IMMUNE SYSTEM / camelid / single domain antibody / dimer / amyloid-like | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Legler, P.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proteins / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u05.cif.gz | 63 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u05.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 4u05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u05_validation.pdf.gz | 432.8 KB | Display | wwPDB validaton report |
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Full document | 4u05_full_validation.pdf.gz | 433.5 KB | Display | |
Data in XML | 4u05_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 4u05_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/4u05 ftp://data.pdbj.org/pub/pdb/validation_reports/u0/4u05 | HTTPS FTP |
-Related structure data
Related structure data | 4tyuSC 4u7sC 4w68C 4w70C 4w81C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 14371.058 Da / Num. of mol.: 2 / Mutation: S74A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Plasmid: pet15b / Details (production host): Cytoplasmic / Production host: Escherichia coli BL21(DE3) (bacteria) #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.24 % / Description: rod-shaped |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 2.5 Details: 0.1 M Citric Acid pH 2.5 1.6 M Ammonium Sulfate 20% Glycerol |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Apr 8, 2012 |
Radiation | Monochromator: BRUKER HELIOS OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→58.58 Å / Num. obs: 10160 / % possible obs: 99.6 % / Redundancy: 7.61 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.19 / Rsym value: 0.188 / Net I/σ(I): 8.05 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.4374 / Mean I/σ(I) obs: 3.95 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TYU Resolution: 2.5→58.58 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.892 / Cross valid method: THROUGHOUT / ESU R: 0.65 / ESU R Free: 0.281 / 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: 11.561 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→58.58 Å
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Refine LS restraints |
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