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- PDB-2tss: TOXIC SHOCK SYNDROME TOXIN-1 FROM STAPHYLOCOCCUS AUREUS: ORTHORHO... -

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Basic information

Entry
Database: PDB / ID: 2tss
TitleTOXIC SHOCK SYNDROME TOXIN-1 FROM STAPHYLOCOCCUS AUREUS: ORTHORHOMBICC222(1) CRYSTAL FORM
ComponentsTOXIC SHOCK SYNDROME TOXIN-1
KeywordsTOXIN / SUPERANTIGEN
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. / 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) ...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) / 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 / MIR / Resolution: 2.05 Å
AuthorsPrasad, G.S. / Radhakrishnan, R. / Mitchell, D.T. / Earhart, C.A. / Dinges, M.M. / Cook, W.J. / Schlivert, P.M. / Ohlendorf, D.H.
Citation
Journal: Protein Sci. / Year: 1997
Title: Refined structures of three crystal forms of toxic shock syndrome toxin-1 and of a tetramutant with reduced activity.
Authors: Prasad, G.S. / Radhakrishnan, R. / Mitchell, D.T. / Earhart, C.A. / Dinges, M.M. / Cook, W.J. / Schlievert, P.M. / Ohlendorf, D.H.
#1: Journal: Biochemistry / Year: 1993
Title: Structure of Toxic Shock Syndrome Toxin 1
Authors: Prasad, G.S. / Earhart, C.A. / Murray, D.L. / Novick, R.P. / Schlievert, P.M. / Ohlendorf, D.H.
History
DepositionDec 4, 1996Processing site: BNL
SupersessionDec 24, 1997ID: 1TSS
Revision 1.0Dec 24, 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water7,296405
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)108.700, 177.500, 97.600
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(0.47228, -0.88134, 0.01424), (-0.88081, -0.47249, -0.03038), (0.0335, 0.0018, -0.99944)79.645, 134.87601, 79.799
2given(-0.57916, -0.81504, 0.0165), (-0.81503, 0.57849, -0.03285), (0.01723, -0.03247, -0.99932)79.057, 42.11, 65.008

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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) / References: UniProt: P06886
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 3.54 Å3/Da / Density % sol: 65 %
Crystal growpH: 4.5
Details: 50-100 MM CITRATE-PHOSPHATE OR ACETATE BUFFER, PH 4-5, 4-8% PEG 4000, 0.25-1M LICL, pH 4.5
PH range: 4-5
Crystal grow
*PLUS
Temperature: 4,18 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150-100 mMcitrate-phosphate1reservoiror acetate
24-8 %PEG40001reservoir
30.25-1 M1reservoirLiCl
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1992
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. obs: 56673 / % possible obs: 94 % / Redundancy: 3.8 % / Rsym value: 0.067 / Net I/σ(I): 7.9
Reflection shellResolution: 2.05→2.17 Å / Redundancy: 2.71 % / Mean I/σ(I) obs: 1 / Rsym value: 0.294 / % possible all: 83
Reflection
*PLUS
Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 83 % / Rmerge(I) obs: 0.294

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.1refinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.05→5 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.154 --
obs0.154 48746 88.4 %
Displacement parametersBiso mean: 24.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.05→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4702 0 0 405 5107
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.26
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.021.5
X-RAY DIFFRACTIONx_mcangle_it32
X-RAY DIFFRACTIONx_scbond_it3.92
X-RAY DIFFRACTIONx_scangle_it5.712.5
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 2.05→2.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.229 1523 -
obs--72.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
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_deg24.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.26
LS refinement shell
*PLUS
Rfactor obs: 0.229

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