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- PDB-3mfg: Crystal structure of Toxic Shock Syndrome Toxin 1 (TSST-1) in com... -

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Basic information

Entry
Database: PDB / ID: 3mfg
TitleCrystal structure of Toxic Shock Syndrome Toxin 1 (TSST-1) in complex with the human T cell receptor beta chain Vbeta2.1 (EP-8)
Components
  • Toxic shock syndrome toxin-1
  • V_segment translation product
KeywordsTOXIN/IMMUNE SYSTEM / Bacterial Toxins / Enterotoxins / Epitopes / Protein Binding / Receptors / Antigen / T-Cell / alpha-beta / Signal Transduction / Superantigens / T-Cell Antigen Receptor Specificity / TOXIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / cell surface receptor signaling pathway / extracellular region / plasma membrane
Similarity search - Function
Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Toxic shock syndrome toxin-1 / T cell receptor beta variable 20-1 / Toxic shock syndrome toxin-1
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsBonsor, D.A. / Sundberg, E.J.
CitationJournal: To be Published
Title: Crystal structure of Toxic Shock Syndrome Toxin 1 (TSST-1) in complex with the human T cell receptor beta chain Vbeta2.1 (EP-8)
Authors: Bonsor, D.A. / Sundberg, E.J.
History
DepositionApr 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...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 / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxic shock syndrome toxin-1
B: V_segment translation product
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3006
Polymers34,9202
Non-polymers3804
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Toxic shock syndrome toxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2002
Polymers22,1041
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: V_segment translation product
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1014
Polymers12,8161
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)242.620, 242.620, 47.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Toxic shock syndrome toxin-1


Mass: 22103.770 Da / Num. of mol.: 1 / Fragment: residues 21-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: N315 / Gene: tst, SA1819 / Plasmid: pET41a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: Q7A4K7, UniProt: A0A0H3JMU6*PLUS
#2: Protein V_segment translation product


Mass: 12816.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCRBV2S1 / Plasmid: pET41a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: A0A5B4*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 4.97 Å3/Da / Density % sol: 75.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.48M Lithium Sulfate, 22% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 27, 2009
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.369→47.582 Å / Num. all: 28994 / Num. obs: 28994 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.9 % / Rsym value: 0.134
Reflection shellResolution: 2.37→2.5 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 4118 / Rsym value: 0.99 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IJ0

2ij0


Resolution: 2.37→47.58 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.881 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.801 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.21 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1473 5.1 %RANDOM
Rwork0.234 ---
all0.237 28972 --
obs0.237 27499 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.68 Å2 / Biso mean: 32.734 Å2 / Biso min: 11.19 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.37→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 21 60 2445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222440
X-RAY DIFFRACTIONr_bond_other_d0.0010.021639
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.9673307
X-RAY DIFFRACTIONr_angle_other_deg0.97834025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7215299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19124.54599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39715424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.889158
X-RAY DIFFRACTIONr_chiral_restr0.1180.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212643
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02469
X-RAY DIFFRACTIONr_mcbond_it1.1781.51502
X-RAY DIFFRACTIONr_mcbond_other0.2381.5605
X-RAY DIFFRACTIONr_mcangle_it2.22822441
X-RAY DIFFRACTIONr_scbond_it3.0473938
X-RAY DIFFRACTIONr_scangle_it4.9474.5865
LS refinement shellResolution: 2.369→2.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 117 -
Rwork0.365 1937 -
all-2054 -
obs--98.75 %

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