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- PDB-1b88: V-ALPHA 2.6 MOUSE T CELL RECEPTOR (TCR) DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1b88
TitleV-ALPHA 2.6 MOUSE T CELL RECEPTOR (TCR) DOMAIN
ComponentsT CELL RECEPTOR V-ALPHA DOMAIN
KeywordsIMMUNE SYSTEM / T CELL RECEPTOR / MHC CLASS I / HUMAN IMMUNODEFICIENCY VIRUS / MOLECULAR RECOGNITION
Function / homology
Function and homology information


T cell receptor complex / peptide antigen binding
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPlaksin, 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
DepositionFeb 9, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T CELL RECEPTOR V-ALPHA DOMAIN
B: T CELL RECEPTOR V-ALPHA DOMAIN


Theoretical massNumber of molelcules
Total (without water)25,3982
Polymers25,3982
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.987, 76.187, 88.402
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9341, 0.352093, -0.059063), (0.354109, -0.934792, 0.027753), (-0.04544, -0.046838, -0.997868)
Vector: -11.3333, 68.8241, 53.3791)

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Components

#1: Protein T CELL RECEPTOR V-ALPHA DOMAIN / TCR


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 / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.76 Å3/Da / Density % sol: 67 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: SODIUM FORMATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM FORMATE11
2SODIUM FORMATE12
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDCrystal-ID
11
21

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 15, 1995
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 13408 / % possible obs: 88.8 % / Redundancy: 13 % / Rmerge(I) obs: 0.127
Reflection shellResolution: 2.5→2.6 Å / % possible all: 39.1
Reflection
*PLUS
Num. measured all: 174142
Reflection shell
*PLUS
% possible obs: 39.1 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TCR

1tcr


Resolution: 2.5→10 Å / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.324 617 5 %RANDOM
Rwork0.224 ---
obs-12193 88.8 %-
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 0 72 2260
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.729
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.89
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.282
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.EAPTOPH.EAP
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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.89
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.282

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