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- PDB-4tul: Crystal structure of monoclonal antibody against neuroblastoma as... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4tul | ||||||
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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 / ACETATE ION![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Golik, P. / Grudnik, P. / Dubin, G. / Zdzalik, M. / Rokita, H. / Horwacik, I. | ||||||
![]() | ![]() 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 | ![]() | 106.2 KB | Display | ![]() |
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PDB format | ![]() | 78.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.7 KB | Display | ![]() |
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Full document | ![]() | 454.5 KB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4trpC ![]() 4tujC ![]() 4tukC ![]() 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
-Protein/peptide , 1 types, 1 molecules I
#3: Protein/peptide | Mass: 1633.843 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Antibody , 2 types, 2 molecules HL
#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.) ![]() ![]() ![]() ![]() |
-Non-polymers , 3 types, 304 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: MES, PEG 5000, NH4SO4 / PH range: 6.5 |
-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: 1.4→77.83 Å / Num. obs: 81806 / % possible obs: 98.96 % / Redundancy: 2 % / Rmerge(I) obs: 0.0292 / Net I/σ(I): 14.52 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 2 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 3.98 / % possible all: 99.87 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1F8T Resolution: 1.4→77.83 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.193 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.067 / 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: 15.237 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→77.83 Å
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Refine LS restraints |
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