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- PDB-2qil: TOXIC SHOCK SYNDROME TOXIN-1 AT 2.07 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 2qil
TitleTOXIC SHOCK SYNDROME TOXIN-1 AT 2.07 A RESOLUTION
ComponentsTOXIC SHOCK SYNDROME TOXIN-1
KeywordsSTAPHYLOCOCCAL ENTEROTOXIN / SUPERANTIGEN / TOXIC SHOCK SYNDROME TOXIN
Function / homology
Function and homology information


toxin activity / extracellular region
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 / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll ...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 / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Toxic shock syndrome toxin-1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.07 Å
AuthorsAcharya, K.R. / Papageorgiou, A.C.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: The refined crystal structure of toxic shock syndrome toxin-1 at 2.07 A resolution.
Authors: Papageorgiou, A.C. / Brehm, R.D. / Leonidas, D.D. / Tranter, H.S. / Acharya, K.R.
#1: Journal: Bacterial Superantigens: Structure, Function and Therapeutic Potential
Year: 1995
Title: Molecular Topology is Important for the Function of Staphylococcal Superantigens
Authors: Tranter, H. / Brehm, R.D. / Acharya, K.R.
#2: Journal: Structure / Year: 1995
Title: Crystal Structure of the Superantigen Enterotoxin C2 from Staphylococcus Aureus Reveals a Zinc-Binding Site
Authors: Papageorgiou, A.C. / Acharya, K.R. / Shapiro, R. / Passalacqua, E.F. / Brehm, R.D. / Tranter, H.S.
#3: Journal: Nature / Year: 1994
Title: Structural Basis of Superantigen Action Inferred from Crystal Structure of Toxic-Shock Syndrome Toxin-1
Authors: Acharya, K.R. / Passalacqua, E.F. / Jones, E.Y. / Harlos, K. / Stuart, D.I. / Brehm, R.D. / Tranter, H.S.
History
DepositionMar 27, 1997Processing site: BNL
Revision 1.0Aug 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _software.name

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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: TOXIC SHOCK SYNDROME TOXIN-1
C: TOXIC SHOCK SYNDROME TOXIN-1


Theoretical massNumber of molelcules
Total (without water)66,3113
Polymers66,3113
Non-polymers00
Water3,207178
1
A: TOXIC SHOCK SYNDROME TOXIN-1


Theoretical massNumber of molelcules
Total (without water)22,1041
Polymers22,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TOXIC SHOCK SYNDROME TOXIN-1


Theoretical massNumber of molelcules
Total (without water)22,1041
Polymers22,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TOXIC SHOCK SYNDROME TOXIN-1


Theoretical massNumber of molelcules
Total (without water)22,1041
Polymers22,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.560, 177.600, 98.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.44572, 0.89496, 0.01933), (-0.89459, -0.44611, 0.02642), (0.03227, -0.00551, 0.99946)26.12599, 132.08661, -32.78778
2given(-0.57444, -0.81835, -0.01794), (-0.81839, 0.57375, 0.03242), (-0.01624, 0.03331, -0.99931)79.54371, 40.0697, 63.3305

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Components

#1: Protein TOXIC SHOCK SYNDROME TOXIN-1 / / TSST-1


Mass: 22103.770 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: MN8 / References: UniProt: P06886
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 60 %
Description: THREE DATA SETS WERE COLLECTED AND MERGED TO GIVE A MASTER DATA SET USED DURING REFINEMENT.
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
223-25 %PEG33501reservoir
30.2 Mammonium sulfate1reservoir
40.2 %1reservoirNaN3
50.1 Msodium acetate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.542
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionNum. obs: 52377 / % possible obs: 89.5 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.086
Reflection
*PLUS
Highest resolution: 2.07 Å / Lowest resolution: 50 Å / Num. measured all: 257472

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
Agrovatadata scaling
X-PLOR3.1phasing
RefinementResolution: 2.07→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.204 -
obs0.204 51240
Displacement parametersBiso mean: 28.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.07→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4677 0 0 178 4855
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.63
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.1
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_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.1
X-RAY DIFFRACTIONx_improper_angle_deg1.35

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