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- PDB-5vl2: The hapten triclocarban bound to the single domain camelid nanobo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vl2 | ||||||
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Title | The hapten triclocarban bound to the single domain camelid nanobody VHH T4 | ||||||
![]() | T4 nanobody | ||||||
![]() | UNKNOWN FUNCTION / ![]() ![]() | ||||||
Function / homology | N-(4-chlorophenyl)-N'-(3,4-dichlorophenyl)urea![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tabares-da Rosa, S. / Gonzalez-Sapienza, G. / Wilson, D.K. | ||||||
![]() | ![]() Title: Structure and specificity of several triclocarban-binding single domain camelid antibody fragments. Authors: Tabares-da Rosa, S. / Wogulis, L.A. / Wogulis, M.D. / Gonzalez-Sapienza, G. / Wilson, D.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 194.5 KB | Display | ![]() |
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PDB format | ![]() | 162.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 14200.888 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-9EG / ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.79 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: Drop contained 1 ul 25 mg/ml protein and 2 ul well. Well contained 0.2 M ammonium sulfate, 0.1 M sodium acetate, 30% w/v PEG MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→96.12 Å / Num. obs: 80496 / % possible obs: 98 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 0.974 / Mean I/σ(I) obs: 2.2 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.93 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→96.12 Å
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Refine LS restraints |
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