+Open data
-Basic information
Entry | Database: PDB / ID: 1tvd | ||||||
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Title | VARIABLE DOMAIN OF T CELL RECEPTOR DELTA CHAIN | ||||||
Components | T CELL RECEPTORT-cell receptor | ||||||
Keywords | IMMUNORECEPTOR / TCR / DELTA CHAIN / VARIABLE DOMAIN | ||||||
Function / homology | Function and homology information T cell receptor complex / adaptive immune response / immune response / innate immune response / extracellular space Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.9 Å | ||||||
Authors | Li, H.M. / Lebedeva, M.I. / Llera, A.S. / Fields, B.A. / Brenner, M.B. / Mariuzza, R.A. | ||||||
Citation | Journal: Nature / Year: 1998 Title: Structure of the Vdelta domain of a human gammadelta T-cell antigen receptor. Authors: Li, H. / Lebedeva, M.I. / Llera, A.S. / Fields, B.A. / Brenner, M.B. / Mariuzza, R.A. #1: Journal: Protein Sci. / Year: 1996 Title: Cloning, Expression, and Crystallization of the V Delta Domain of a Human Gamma Delta T-Cell Receptor Authors: Lebedeva, M.I. / Fields, B.A. / Spits, H. / Panchamoorthy, G. / Brenner, M.B. / Mariuzza, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tvd.cif.gz | 61.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tvd.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 1tvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/1tvd ftp://data.pdbj.org/pub/pdb/validation_reports/tv/1tvd | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: (-0.971829, -0.032294, -0.233465), Vector: |
-Components
#1: Protein | Mass: 13145.624 Da / Num. of mol.: 2 / Fragment: DELTA CHAIN, VARIABLE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: T-LYMPHOCYTE / Cell line: ES204 / Plasmid: PET26B(+) / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 BL21 (DE3) / References: PIR: S04934, UniProt: A0JD37*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 0.65-0.75M SODIUM CITRATE 0.1M SODIUM CACODYLATE, PH 6.5 | ||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Lebedeva, M.I., (1996) Protein Sci., 5, 2638. / pH: 7 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 278 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 |
Detector | Type: SIEMENS / Detector: CCD / Date: Jun 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→99 Å / Num. obs: 44342 / % possible obs: 83.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 3 / Rsym value: 0.166 / % possible all: 53.7 |
Reflection | *PLUS Num. obs: 13905 / Num. measured all: 44342 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 1.9→6 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 14.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Total num. of bins used: 15
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.174 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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