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Open data
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Basic information
Entry | Database: PDB / ID: 6s2i | |||||||||
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Title | Anti-tumor antibody 14F7-derived scFv in complex with NeuGc Gm3 | |||||||||
![]() | scFv C1 | |||||||||
![]() | ANTITUMOR PROTEIN / ganglioside / complex / scfv / antibody fragment / single chain fragment variable / immuno therapy / 14F7 / gm3 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bjerregaard-Andersen, K. / Heggelund, J.E. / Krengel, U. | |||||||||
![]() | ![]() Title: Key role of a structural water molecule for the specificity of 14F7-An antitumor antibody targeting the NeuGc GM3 ganglioside. Authors: Bjerregaard-Andersen, K. / Abraha, F. / Johannesen, H. / Oscarson, S. / Moreno, E. / Krengel, U. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 208.1 KB | Display | ![]() |
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PDB format | ![]() | 157.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 859.1 KB | Display | ![]() |
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Full document | ![]() | 865.9 KB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ffjS 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: 28116.238 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | N-glycolyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose | Type: oligosaccharide / Mass: 649.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.11 % / Description: Plates |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 12.5 % w/v PEG 1000, 12.5 % w/v PEG 3350, 12.5 % v/v MPD, 0.02 M 1,6-hexandiol, 0.02 M 1-butanol, 0.02 M (RS)-1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3- ...Details: 12.5 % w/v PEG 1000, 12.5 % w/v PEG 3350, 12.5 % v/v MPD, 0.02 M 1,6-hexandiol, 0.02 M 1-butanol, 0.02 M (RS)-1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3-propanediol, 0.1 M bicine/tris base pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.285→62.9 Å / Num. obs: 42116 / % possible obs: 98.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 44.029 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.053 / Rrim(I) all: 0.111 / Net I/σ(I): 9.03 |
Reflection shell | Resolution: 2.285→2.325 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2141 / CC1/2: 0.813 / Rpim(I) all: 0.379 / Rrim(I) all: 0.795 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6FFJ Resolution: 2.285→62.865 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.285→62.865 Å
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Refine LS restraints |
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LS refinement shell |
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