+Open data
-Basic information
Entry | Database: PDB / ID: 2p1y | ||||||
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Title | 1.B2.D9, a bispecific alpha/beta TCR | ||||||
Components | bispecific alpha/beta TCR | ||||||
Keywords | IMMUNE SYSTEM / TCR / autoimmunity / immunoglobulin fold / diabody | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | ||||||
Authors | McBeth, C. / Pizarro, J.C. / Strong, R.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: A new twist in TCR diversity revealed by a forbidden alphabeta TCR. Authors: McBeth, C. / Seamons, A. / Pizarro, J.C. / Fleishman, S.J. / Baker, D. / Kortemme, T. / Goverman, J.M. / Strong, R.K. | ||||||
History |
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Remark 999 | sequence The alpha and beta chains were cloned in single chain format with the C-terminus of the ...sequence The alpha and beta chains were cloned in single chain format with the C-terminus of the beta chain extending to the N-terminus of the alpha chain. The numbering is standard Kabat numbering (immunology protocol) throughout with the beta chain starting around 1, the linker +200, and the alpha chain +300. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p1y.cif.gz | 182.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p1y.ent.gz | 146 KB | Display | PDB format |
PDBx/mmJSON format | 2p1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p1y_validation.pdf.gz | 452.1 KB | Display | wwPDB validaton report |
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Full document | 2p1y_full_validation.pdf.gz | 471.9 KB | Display | |
Data in XML | 2p1y_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 2p1y_validation.cif.gz | 47.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/2p1y ftp://data.pdbj.org/pub/pdb/validation_reports/p1/2p1y | HTTPS FTP |
-Related structure data
Related structure data | 2p24C 1u3hS C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 26267.268 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: 1.B2.D9 / Gene: Valpha2.3/Vbeta8.2 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 (RIL) / References: UniProt: Q5R1B3*PLUS #2: 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: 2.63 Å3/Da / Density % sol: 53.31 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12% w/w PEG 6000, 100 mM HEPES, 3% v/v MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 3, 2004 |
Radiation | Monochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→40.4 Å / Num. all: 41336 / Num. obs: 41336 / % possible obs: 99.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.42→2.51 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 6.29 / Num. unique all: 4017 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1U3H Resolution: 2.42→40.39 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.901 / SU B: 7.666 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.269 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.916 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.42→40.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.42→2.484 Å / Total num. of bins used: 20
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