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- PDB-1bec: BETA CHAIN OF A T CELL ANTIGEN RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 1bec
TitleBETA CHAIN OF A T CELL ANTIGEN RECEPTOR
Components14.3.D T CELL ANTIGEN RECEPTOR
KeywordsRECEPTOR / T CELL RECEPTOR
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsBentley, G.A. / Boulot, G. / Karjalainen, K. / Mariuzza, R.A.
Citation
Journal: Science / Year: 1995
Title: Crystal structure of the beta chain of a T cell antigen receptor.
Authors: Bentley, G.A. / Boulot, G. / Karjalainen, K. / Mariuzza, R.A.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallisation and Preliminary X-Ray Diffraction Analysis of the Beta Chain of a T-Cell Antigen Receptor
Authors: Boulot, G. / Bentley, G.A. / Karjalainen, K. / Mariuzza, R.A.
History
DepositionFeb 28, 1995Processing site: BNL
Revision 1.0Oct 25, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 17, 2019Group: Atomic model / Data collection / Refinement description
Category: atom_site / software
Item: _atom_site.occupancy / _software.classification / _software.name
Revision 2.1Aug 14, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / pdbx_validate_symm_contact / software
Item: _software.classification / _software.name
Revision 2.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14.3.D T CELL ANTIGEN RECEPTOR


Theoretical massNumber of molelcules
Total (without water)26,5681
Polymers26,5681
Non-polymers00
Water1,964109
1
A: 14.3.D T CELL ANTIGEN RECEPTOR

A: 14.3.D T CELL ANTIGEN RECEPTOR


Theoretical massNumber of molelcules
Total (without water)53,1372
Polymers53,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)100.600, 36.600, 71.500
Angle α, β, γ (deg.)90.00, 113.40, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO 8 / 2: CIS PROLINE - PRO 154
Components on special symmetry positions
IDModelComponents
11A-337-

HOH

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Components

#1: Protein 14.3.D T CELL ANTIGEN RECEPTOR


Mass: 26568.490 Da / Num. of mol.: 1 / Mutation: N24Q, N74Q, N121Q, N236V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: J558L / Production host: Mus musculus (house mouse) / References: UniProt: Q8K1Z5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15.8 mg/mlprotein1drop
27.3 mMTris1drop
325 mMHEPES1drop
418.3 mM1dropNaCl
51.0 %(w/v)PEG40001dropdrop
60.75 %satammonium sulfate1
70.014 %agarose1drop
84 %PEG40001reservoir
90.1 MHEPES1reservoir
103 %ammonium sulfate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1994
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionRedundancy: 2.4 % / Rmerge(I) obs: 0.049
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 15 Å / Num. obs: 25371 / % possible obs: 95.6 % / Num. measured all: 60827 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.76 Å / % possible obs: 95.1 % / Rmerge(I) obs: 0.399

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Processing

Software
NameClassification
XDSdata scaling
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
XDSdata reduction
X-PLORphasing
RefinementResolution: 1.7→7 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.198 -
obs0.198 21745
Refinement stepCycle: LAST / Resolution: 1.7→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 0 109 1935
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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

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