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- PDB-1ts4: Q139K MUTANT OF TOXIC SHOCK SYNDROME TOXIN-1 FROM S. AUREUS -

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Basic information

Entry
Database: PDB / ID: 1ts4
TitleQ139K MUTANT OF TOXIC SHOCK SYNDROME TOXIN-1 FROM S. AUREUS
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 / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsEarhart, C.A. / Mitchell, D.T. / Murray, D.L. / Pinheiro, D.M. / Matsumura, M. / Schlievert, P.M. / Ohlendorf, D.H.
Citation
Journal: Biochemistry / Year: 1998
Title: Structures of five mutants of toxic shock syndrome toxin-1 with reduced biological activity.
Authors: Earhart, C.A. / Mitchell, D.T. / Murray, D.L. / Pinheiro, D.M. / Matsumura, M. / Schlievert, P.M. / Ohlendorf, D.H.
#1: 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.
#2: 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
DepositionOct 10, 1997Processing site: BNL
Revision 1.0Dec 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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


Theoretical massNumber of molelcules
Total (without water)44,2102
Polymers44,2102
Non-polymers00
Water00
1
A: TOXIC SHOCK SYNDROME TOXIN-1


Theoretical massNumber of molelcules
Total (without water)22,1051
Polymers22,1051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TOXIC SHOCK SYNDROME TOXIN-1


Theoretical massNumber of molelcules
Total (without water)22,1051
Polymers22,1051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)152.350, 152.350, 142.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.817232, -0.222338, -0.531694), (-0.201364, -0.974597, 0.098043), (-0.539986, 0.02694, -0.841243)
Vector: 61.38042, 132.92462, 154.79849)

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Components

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


Mass: 22104.820 Da / Num. of mol.: 2 / Mutation: Q139K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Staphylococcus aureus (bacteria) / References: UniProt: P06886

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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: 3.59 Å3/Da / Density % sol: 65.77 %
Crystal growpH: 4 / Details: pH 4
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMacetate1reservoir
34-16 %PEG40001reservoir
41 M1reservoirLiCl
5100-200 mM1reservoirMgCl2

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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: Mar 1, 1997
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→20 Å / Num. obs: 64169 / % possible obs: 99 % / Redundancy: 7.8 % / Rsym value: 0.149 / Net I/σ(I): 6.1
Reflection shellResolution: 3.4→3.6 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1 / Rsym value: 0.36 / % possible all: 100
Reflection
*PLUS
Num. obs: 8172 / Num. measured all: 64169 / Rmerge(I) obs: 0.149
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.36

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TSS

1tss
PDB Unreleased entry


Resolution: 3.4→20 Å / Data cutoff high absF: 100000000 / Data cutoff low absF: 0 / Cross valid method: FREE R / σ(F): 0
Details: BECAUSE OF RESOLUTION, RWEIGHT WAS INCREASED BY A FACTOR OF 5 WHILE TARGET SIGMAS WERE DECREASED BY A FACTOR OF 5.
RfactorNum. reflection% reflection
Rfree0.287 -5 %
Rwork0.21 --
obs0.21 7865 -
Displacement parametersBiso mean: 55.71 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 3.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3118 0 0 0 3118
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.022
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_deg2.37
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
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_it0.540.3
X-RAY DIFFRACTIONx_mcangle_it1.030.4
X-RAY DIFFRACTIONx_scbond_it0.170.4
X-RAY DIFFRACTIONx_scangle_it0.440.5
LS refinement shellResolution: 3.4→3.5 Å / Total num. of bins used: 20 /
Rfactor% reflection
Rfree0.41 5 %
Rwork0.319 -
obs-28 %
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.319

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