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- PDB-2apt: Crystal Structure of the G17E/S54N/K66E/Q72H/E80V/L81S/T87S/G96V ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2apt | ||||||
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Title | Crystal Structure of the G17E/S54N/K66E/Q72H/E80V/L81S/T87S/G96V variant of the murine T cell receptor V beta 8.2 domain | ||||||
![]() | T-cell receptor beta chain V | ||||||
![]() | IMMUNE SYSTEM / the murine T cell receptor V beta 8.2 domain | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Cho, S. / Swaminathan, C.P. / Yang, J. / Kerzic, M.C. / Guan, R. / Kieke, M.C. / Kranz, D.M. / Mariuzza, R.A. / Sundberg, E.J. | ||||||
![]() | ![]() Title: Structural basis of affinity maturation and intramolecular cooperativity in a protein-protein interaction. Authors: Cho, S. / Swaminathan, C.P. / Yang, J. / Kerzic, M.C. / Guan, R. / Kieke, M.C. / Kranz, D.M. / Mariuzza, R.A. / Sundberg, E.J. | ||||||
History |
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Remark 999 | SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE AT THE TIME OF PROCESSING THIS FILE. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.9 KB | Display | ![]() |
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PDB format | ![]() | 41.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.1 KB | Display | ![]() |
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Full document | ![]() | 451 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2apbC ![]() 2apfC ![]() 2apvC ![]() 2apwC ![]() 2apxC ![]() 2aq1C ![]() 2aq2C ![]() 2aq3C 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12156.431 Da / Num. of mol.: 2 / Mutation: G17E, S54N, K66E, Q72H, E80V, L81S, T87S, G96V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MLA / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 59.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.0 M Sodium Malonate, 0.2 % dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 10, 2003 / Details: mirrors |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→34.4 Å / Num. all: 20008 / Num. obs: 18476 / % possible obs: 92.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 |
Reflection shell | Resolution: 2→2.05 Å / % possible all: 65.4 |
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Processing
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Refinement | Method to determine structure: ![]() Details: The residues Gly 63 and Tyr 65 of chain B should be linked according to the sequence database reference. However the C-N bond distance is 2.00 A
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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: 39.722 Å2
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Refinement step | Cycle: LAST / Resolution: 2→34.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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