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- PDB-2p1y: 1.B2.D9, a bispecific alpha/beta TCR -

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Basic information

Entry
Database: PDB / ID: 2p1y
Title1.B2.D9, a bispecific alpha/beta TCR
Componentsbispecific alpha/beta TCR
KeywordsIMMUNE SYSTEM / TCR / autoimmunity / immunoglobulin fold / diabody
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsMcBeth, C. / Pizarro, J.C. / Strong, R.K.
CitationJournal: 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
DepositionMar 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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
Remark 999sequence 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: bispecific alpha/beta TCR
C: bispecific alpha/beta TCR
E: bispecific alpha/beta TCR
G: bispecific alpha/beta TCR


Theoretical massNumber of molelcules
Total (without water)105,0694
Polymers105,0694
Non-polymers00
Water1,838102
1
A: bispecific alpha/beta TCR
C: bispecific alpha/beta TCR


Theoretical massNumber of molelcules
Total (without water)52,5352
Polymers52,5352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: bispecific alpha/beta TCR
G: bispecific alpha/beta TCR


Theoretical massNumber of molelcules
Total (without water)52,5352
Polymers52,5352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.681, 105.477, 81.531
Angle α, β, γ (deg.)90.00, 116.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
bispecific alpha/beta TCR


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 / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 3, 2004
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1U3H

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
RfactorNum. reflection% reflectionSelection details
Rfree0.25363 2073 5 %RANDOM
Rwork0.18142 ---
obs0.18508 39252 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.916 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refine analyze
FreeObs
Luzzati sigma a0.269 Å0.376 Å
Refinement stepCycle: LAST / Resolution: 2.42→40.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6915 0 0 102 7017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0227093
X-RAY DIFFRACTIONr_angle_refined_deg2.5291.9379619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg16.5615885
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.11724.509326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.371151106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4231525
X-RAY DIFFRACTIONr_chiral_restr0.1910.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025465
X-RAY DIFFRACTIONr_nbd_refined0.2290.22463
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24437
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2417
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.225
X-RAY DIFFRACTIONr_mcbond_it2.2351.54640
X-RAY DIFFRACTIONr_mcangle_it2.84427083
X-RAY DIFFRACTIONr_scbond_it5.07332952
X-RAY DIFFRACTIONr_scangle_it6.5034.52536
LS refinement shellResolution: 2.42→2.484 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 151 -
Rwork0.201 2867 -
obs--99.37 %

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