+Open data
-Basic information
Entry | Database: PDB / ID: 4grm | ||||||
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Title | The crystal structure of the high affinity TCR A6 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / high-affinity TCR / c134 modification / TAX peptide / nonapeptide / MHC class I / HLA-A2 / TCR A6 / cross-reactivity | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Borbulevych, O.Y. / Scott, D.R. / Baker, B.M. | ||||||
Citation | Journal: Front Immunol / Year: 2013 Title: Increased Peptide Contacts Govern High Affinity Binding of a Modified TCR Whilst Maintaining a Native pMHC Docking Mode. Authors: Cole, D.K. / Sami, M. / Scott, D.R. / Rizkallah, P.J. / Borbulevych, O.Y. / Todorov, P.T. / Moysey, R.K. / Jakobsen, B.K. / Boulter, J.M. / Baker, B.M. / Li, Y.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4grm.cif.gz | 171.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4grm.ent.gz | 141.7 KB | Display | PDB format |
PDBx/mmJSON format | 4grm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/4grm ftp://data.pdbj.org/pub/pdb/validation_reports/gr/4grm | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 21395.467 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #2: Protein | Mass: 27452.533 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.45 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% PEG, 0.1 M TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Oct 21, 2009 |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 58107 / Num. obs: 57468 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 2.12 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→18.84 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.775 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.21 / Stereochemistry target values: Engh & Huber
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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: 42.939 Å2
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Refinement step | Cycle: LAST / Resolution: 2→18.84 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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