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- PDB-4tss: TOXIC SHOCK SYNDROME TOXIN-1: TETRAGONAL P4(1)2(1)2 CRYSTAL FORM -

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Basic information

Entry
Database: PDB / ID: 4tss
TitleTOXIC SHOCK SYNDROME TOXIN-1: TETRAGONAL P4(1)2(1)2 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 / MOLECULAR REPLACEMENT / Resolution: 2.75 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 11, 1996Processing site: BNL
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 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TOXIC SHOCK SYNDROME TOXIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1692
Polymers22,1041
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.300, 47.300, 205.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 22103.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PURCHASED FROM TOXIN TECHNOLOGIES / Source: (natural) Staphylococcus aureus (bacteria) / Cellular location: SECRETED / Strain: MN 8 / References: UniProt: P06886
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growpH: 6
Details: 14% PEG 8000, 0.2 M ZN ACETATE, 0.1 M NA CACODYLATE, PH 6, pH 6.0
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 %PEG80001reservoir
20.2 Mzinc acetate1reservoir
30.1 MNa-cacodylate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1994
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.18→45.8 Å / Num. obs: 6274 / % possible obs: 50 % / Redundancy: 3.15 % / Rsym value: 0.0675 / Net I/σ(I): 6.45
Reflection shellResolution: 2.75→3 Å / % possible all: 50
Reflection
*PLUS
Rmerge(I) obs: 0.0675
Reflection shell
*PLUS
% possible obs: 50 %

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Processing

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

1tss
PDB Unreleased entry


Resolution: 2.75→5 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.191 --
obs0.191 11409 72.5 %
Displacement parametersBiso mean: 22.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.75→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1559 0 1 0 1560
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.096
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.75
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.911.5
X-RAY DIFFRACTIONx_mcangle_it4.482
X-RAY DIFFRACTIONx_scbond_it4.12
X-RAY DIFFRACTIONx_scangle_it5.622.5
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 2.75→2.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.257 112 -
obs--38.2 %
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_deg24.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.75
LS refinement shell
*PLUS
Rfactor obs: 0.257

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