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- PDB-1sbb: T-CELL RECEPTOR BETA CHAIN COMPLEXED WITH SUPERANTIGEN SEB -

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Basic information

Entry
Database: PDB / ID: 1sbb
TitleT-CELL RECEPTOR BETA CHAIN COMPLEXED WITH SUPERANTIGEN SEB
Components
  • PROTEIN (14.3.D T CELL ANTIGEN RECEPTOR)
  • PROTEIN (STAPHYLOCOCCAL ENTEROTOXIN B)
KeywordsIMMUNE SYSTEM / T CELL RECEPTOR / SUPERANTIGEN / COMPLEX
Function / homology
Function and homology information


alpha-beta T cell receptor complex / toxin activity / extracellular region / metal ion binding
Similarity search - Function
Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain ...Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Superantigen toxin, C-terminal / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / : / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Enterotoxin type B / T-cell receptor beta-1 chain C region
Similarity search - Component
Biological speciesMus musculus (house mouse)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLi, H. / Mariuzza, R.A.
CitationJournal: Immunity / Year: 1998
Title: Three-dimensional structure of the complex between a T cell receptor beta chain and the superantigen staphylococcal enterotoxin B.
Authors: Li, H. / Llera, A. / Tsuchiya, D. / Leder, L. / Ysern, X. / Schlievert, P.M. / Karjalainen, K. / Mariuzza, R.A.
History
DepositionFeb 22, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 1, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (14.3.D T CELL ANTIGEN RECEPTOR)
B: PROTEIN (STAPHYLOCOCCAL ENTEROTOXIN B)
C: PROTEIN (14.3.D T CELL ANTIGEN RECEPTOR)
D: PROTEIN (STAPHYLOCOCCAL ENTEROTOXIN B)


Theoretical massNumber of molelcules
Total (without water)109,9594
Polymers109,9594
Non-polymers00
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.200, 83.650, 82.980
Angle α, β, γ (deg.)90.00, 93.04, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99878, -0.04882, -0.00689), (-0.04923, 0.99529, 0.08352), (0.00278, 0.08376, -0.99648)128.39771, 1.59805, 41.68963
2given(-0.99632, -0.08308, 0.0212), (-0.07446, 0.9609, 0.26668), (-0.04253, 0.26412, -0.96355)129.66364, 3.09364, 35.81734
3given(-0.99296, -0.03119, -0.11425), (-0.03954, 0.99666, 0.07151), (0.11164, 0.07553, -0.99087)127.11024, 1.09422, 35.92722

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Components

#1: Protein PROTEIN (14.3.D T CELL ANTIGEN RECEPTOR)


Mass: 26568.490 Da / Num. of mol.: 2 / Fragment: BETA CHAIN / Mutation: N24Q, N74Q, N121Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) / References: GenBank: 1791255, UniProt: P01852*PLUS
#2: Protein PROTEIN (STAPHYLOCOCCAL ENTEROTOXIN B) / SEB


Mass: 28411.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: RN9220 / Production host: Escherichia coli (E. coli) / References: UniProt: P01552
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 49 %
Crystal growpH: 8.5
Details: CRYSTALLIZATION CONDITIONS: 10% PEG 8000 0.1M TRIS-HCL, PH8.5
Crystal
*PLUS
Density % sol: 6 %
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
29-12 %(w/v)PEG80001reservoir
30.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.928
DetectorType: PRINCETON 2K / Detector: CCD / Date: Aug 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 34934 / % possible obs: 91.5 % / Redundancy: 9 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 17
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4 / Rsym value: 0.36 / % possible all: 79.1
Reflection
*PLUS
Num. measured all: 325939
Reflection shell
*PLUS
% possible obs: 79.1 % / Mean I/σ(I) obs: 4

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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 1SE4 AND 1BEC

1se4

1bec


Resolution: 2.4→6 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.309 2647 8.2 %RANDOM
Rwork0.228 ---
obs-32402 90.8 %-
Displacement parametersBiso mean: 35.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7589 0 0 159 7748
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.08
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
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.4→2.45 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.442 161 6.7 %
Rwork0.356 1690 -
obs--77 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / σ(F): 2 / % reflection Rfree: 8.2 % / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.08
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Rfactor Rfree: 0.442 / % reflection Rfree: 6.7 % / Rfactor Rwork: 0.356

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