+Open data
-Basic information
Entry | Database: PDB / ID: 1b88 | ||||||
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Title | V-ALPHA 2.6 MOUSE T CELL RECEPTOR (TCR) DOMAIN | ||||||
Components | T CELL RECEPTOR V-ALPHA DOMAIN | ||||||
Keywords | IMMUNE SYSTEM / T CELL RECEPTOR / MHC CLASS I / HUMAN IMMUNODEFICIENCY VIRUS / MOLECULAR RECOGNITION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Plaksin, D. / Chacko, S. / Navaza, J. / Margulies, D.H. / Padlan, E.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: The X-ray crystal structure of a Valpha2.6Jalpha38 mouse T cell receptor domain at 2.5 A resolution: alternate modes of dimerization and crystal packing. Authors: Plaksin, D. / Chacko, S. / Navaza, J. / Margulies, D.H. / Padlan, E.A. #1: Journal: J.Exp.Med. / Year: 1996 Title: A T cell receptor V alpha domain expressed in bacteria: does it dimerize in solution? Authors: Plaksin, D. / Chacko, S. / McPhie, P. / Bax, A. / Padlan, E.A. / Margulies, D.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b88.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b88.ent.gz | 49.2 KB | Display | PDB format |
PDBx/mmJSON format | 1b88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b88_validation.pdf.gz | 368.3 KB | Display | wwPDB validaton report |
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Full document | 1b88_full_validation.pdf.gz | 375.8 KB | Display | |
Data in XML | 1b88_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 1b88_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/1b88 ftp://data.pdbj.org/pub/pdb/validation_reports/b8/1b88 | HTTPS FTP |
-Related structure data
Related structure data | 1tcrS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9341, 0.352093, -0.059063), Vector: |
-Components
#1: Protein | Mass: 12699.169 Da / Num. of mol.: 2 / Fragment: V-ALPHA DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell: T LYMPHOCYTE / Cell line: B4.2.3 T CELL HYBRIDOMA / Cellular location: PLASMA MEMBRANE / Gene: TCRAV2S6J38 / Plasmid: PET3A / Species (production host): Escherichia coli / Cellular location (production host): INCLUSION BODIES / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 1518838, 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: 3.76 Å3/Da / Density % sol: 67 % | ||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: SODIUM FORMATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP | ||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: unknown | ||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 15, 1995 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. obs: 13408 / % possible obs: 88.8 % / Redundancy: 13 % / Rmerge(I) obs: 0.127 |
Reflection shell | Resolution: 2.5→2.6 Å / % possible all: 39.1 |
Reflection | *PLUS Num. measured all: 174142 |
Reflection shell | *PLUS % possible obs: 39.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TCR Resolution: 2.5→10 Å / Cross valid method: THROUGHOUT / σ(F): 3
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.224 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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