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Open data
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Basic information
Entry | Database: PDB / ID: 7tjc | |||||||||
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Title | VHH Chl-B2 in complex with Chloramphenicol | |||||||||
![]() | VHH-Chl-B2 | |||||||||
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Function / homology | ![]() ![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Nordeen, S.A. / Schwartz, T.U. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and specificity of an anti-chloramphenicol single domain antibody for detection of amphenicol residues. Authors: Swofford, C.A. / Nordeen, S.A. / Chen, L. / Desai, M.M. / Chen, J. / Springs, S.L. / Schwartz, T.U. / Sinskey, A.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.9 KB | Display | ![]() |
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PDB format | ![]() | 89.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1bzqS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 15035.549 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ChemComp-GOL / | ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43 % / Description: rod-shaped |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 100 mM sodium acetate, 1 M di-ammonium hydrogen phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.35→54.15 Å / Num. obs: 59730 / % possible obs: 99.7 % / Redundancy: 12.7 % / Biso Wilson estimate: 15.26 Å2 / CC1/2: 0.999 / Rpim(I) all: 2.4 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 6000 / CC1/2: 0.739 / Rpim(I) all: 0.398 / % possible all: 98.2 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1BZQ Resolution: 1.35→54.15 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.73 Å2 / Biso mean: 21.71 Å2 / Biso min: 9.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→54.15 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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