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- PDB-5tss: TOXIC SHOCK SYNDROME TOXIN-1: ORTHORHOMBIC P222(1) CRYSTAL FORM -

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Basic information

Entry
Database: PDB / ID: 5tss
TitleTOXIC SHOCK SYNDROME TOXIN-1: ORTHORHOMBIC P222(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 / MOLECULAR REPLACEMENT / Resolution: 2.9 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 1.3Mar 6, 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 / pdbx_database_status / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _refine.pdbx_method_to_determine_struct / _refine.pdbx_starting_model

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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)44,2082
Polymers44,2082
Non-polymers00
Water48627
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
MethodPISA
Unit cell
Length a, b, c (Å)49.100, 75.100, 115.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99889, -0.02139, 0.04192), (0.0392, -0.8711, 0.48953), (0.02604, 0.49063, 0.87098)
Vector: 76.295, 66.865, -25.578)

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Components

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


Mass: 22103.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Cellular location: SECRETED / Strain: MN 8 / References: UniProt: P06886
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTSST-1 IS PRODUCED AS A PRO-PEPTIDE WITH 40 AMINO ACIDS AT ITS AMINO-TERMINUS. THE NUMBERING SCHEME ...TSST-1 IS PRODUCED AS A PRO-PEPTIDE WITH 40 AMINO ACIDS AT ITS AMINO-TERMINUS. THE NUMBERING SCHEME HERE BEGINS WITH THE FIRST RESIDUE OF THE MATURE PROTEIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal growpH: 6.5
Details: 50 MM TRIS-MALATE BUFFER, PH 5.8-6.6, 24% PEG 4000, 0.5-1 M LICL, pH 6.5
PH range: 5.8-6.6
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion / PH range low: 6.6 / PH range high: 5.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMTris-maleate1reservoir
324 %PEG40001reservoir
40.5-1 M1reservoirLiCl

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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: Jul 1, 1992
RadiationMonochromator: YES / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 185649 / % possible obs: 98 % / Redundancy: 18.6 % / Rsym value: 0.108 / Net I/σ(I): 6.6
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1 / Rsym value: 0.376 / % possible all: 87
Reflection
*PLUS
Rmerge(I) obs: 0.108
Reflection shell
*PLUS
% possible obs: 87 % / Rmerge(I) obs: 0.376

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→5 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 1
Details: THE OCCUPANCY FOR SER A 11 THROUGH PRO A 117 IS SET TO ZERO BECAUSE OF THE ABSENCE OF 2FO-FC DENSITY. THIS SEGMENT PARTICIPATES IN A CLOSE CONTACT WITH A TWO-FOLD RELATED MOLECULE. THE ...Details: THE OCCUPANCY FOR SER A 11 THROUGH PRO A 117 IS SET TO ZERO BECAUSE OF THE ABSENCE OF 2FO-FC DENSITY. THIS SEGMENT PARTICIPATES IN A CLOSE CONTACT WITH A TWO-FOLD RELATED MOLECULE. THE CONFORMATION PRESENTED IS SIMILAR TO THAT SEEN IN OTHER CRYSTAL FORMS OF TSST-1.
RfactorNum. reflection% reflection
Rwork0.148 --
obs0.148 7280 92.2 %
Displacement parametersBiso mean: 20 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.9→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4702 0 0 405 5107
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.76
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.39
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.121.5
X-RAY DIFFRACTIONx_mcangle_it4.842
X-RAY DIFFRACTIONx_scbond_it4.852
X-RAY DIFFRACTIONx_scangle_it6.892.5
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.204 689 -
obs--57.2 %
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_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39
LS refinement shell
*PLUS
Rfactor obs: 0.204

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