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- PDB-4tuk: Crystal structure of monoclonal antibody against neuroblastoma as... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4tuk | ||||||
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Title | Crystal structure of monoclonal antibody against neuroblastoma associated antigen. | ||||||
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![]() | IMMUNE SYSTEM / Neuroblastoma | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Golik, P. / Grudnik, P. / Dubin, G. / Horwacik, I. / Zdzalik, M. / Rokita, H. | ||||||
![]() | ![]() Title: Structural Basis of GD2 Ganglioside and Mimetic Peptide Recognition by 14G2a Antibody. Authors: Horwacik, I. / Golik, P. / Grudnik, P. / Kolinski, M. / Zdzalik, M. / Rokita, H. / Dubin, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.6 KB | Display | ![]() |
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PDB format | ![]() | 79.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.2 KB | Display | ![]() |
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Full document | ![]() | 425.2 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 31.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4trpC ![]() 4tujC ![]() 4tulC ![]() 4tuoC ![]() 1f8tS 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: 22748.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 24251.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1633.843 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Hepes, PEG 4000, isopropanol / PH range: 7.1 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→57.09 Å / Num. obs: 46752 / % possible obs: 90.68 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 17.38 |
Reflection shell | Resolution: 1.6→1.657 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.76 / % possible all: 90.66 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1F8T Resolution: 1.6→57.09 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.61 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 17.091 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→57.09 Å
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Refine LS restraints |
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