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Open data
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Basic information
Entry | Database: PDB / ID: 6vth | ||||||
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Title | p53-specific T cell receptor | ||||||
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![]() | IMMUNE SYSTEM / TCR complex / MHC / HLA / adoptive cell therapy | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, D. / Gallagher, D.T. / Gowthaman, R. / Pierce, B.G. / Mariuzza, R.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for oligoclonal T cell recognition of a shared p53 cancer neoantigen. Authors: Wu, D. / Gallagher, D.T. / Gowthaman, R. / Pierce, B.G. / Mariuzza, R.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 345 KB | Display | ![]() |
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PDB format | ![]() | 280.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 264.2 KB | Display | ![]() |
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Full document | ![]() | 264.1 KB | Display | |
Data in XML | ![]() | 1.3 KB | Display | |
Data in CIF | ![]() | 11.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vqoC ![]() 6vr1C ![]() 6vr5C ![]() 6vrmC ![]() 6vrnC ![]() 6vtcC ![]() 2ak4S ![]() 3sjvS S: Starting model for refinement C: citing same article ( |
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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: Protein | Mass: 22881.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 27789.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-SO4 / | #4: 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: 2.44 Å3/Da / Density % sol: 49.51 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 6 / Details: 18% (w/v) PEG 2000, 0.2 M AmSO4, 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→39.3 Å / Num. obs: 36665 / % possible obs: 91.1 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.36→2.44 Å / Rmerge(I) obs: 0.263 / Num. unique obs: 3669 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3sjv, 2ak4 Resolution: 2.36→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.901 / SU B: 14.97 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.54 / ESU R Free: 0.294 / Details: TLS
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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 max: 94.19 Å2 / Biso mean: 39.584 Å2 / Biso min: 18.21 Å2
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Refinement step | Cycle: final / Resolution: 2.36→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.36→2.419 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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