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- PDB-1qil: INACTIVE MUTANT TOXIC SHOCK SYNDROME TOXIN-1 AT 2.5 A -

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Basic information

Entry
Database: PDB / ID: 1qil
TitleINACTIVE MUTANT TOXIC SHOCK SYNDROME TOXIN-1 AT 2.5 A
ComponentsTOXIC SHOCK SYNDROME TOXIN-1
KeywordsTOXIN / SUPERANTIGEN / STAPHYLOCOCCAL ENTEROTOXIN
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 / SYNCHROTRON / Resolution: 2.5 Å
AuthorsAcharya, K.R. / Papageorgiou, A.C.
Citation
Journal: Protein Sci. / Year: 1996
Title: Crystal structure of a biologically inactive mutant of toxic shock syndrome toxin-1 at 2.5 A resolution.
Authors: Papageorgiou, A.C. / Quinn, C.P. / Beer, D. / Brehm, R.D. / Tranter, H.S. / Bonventre, P.F. / 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 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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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)66,1103
Polymers66,1103
Non-polymers00
Water2,216123
1
A: TOXIC SHOCK SYNDROME TOXIN-1


Theoretical massNumber of molelcules
Total (without water)22,0371
Polymers22,0371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TOXIC SHOCK SYNDROME TOXIN-1


Theoretical massNumber of molelcules
Total (without water)22,0371
Polymers22,0371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TOXIC SHOCK SYNDROME TOXIN-1


Theoretical massNumber of molelcules
Total (without water)22,0371
Polymers22,0371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.030, 177.450, 97.510
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(-0.43969, 0.89785, 0.02309), (-0.8973, -0.44025, 0.03202), (0.03892, -0.00664, 0.99922)25.29179, 131.35327, -32.71116
2given(-0.5825, -0.81265, -0.01682), (-0.81266, 0.58183, 0.03265), (-0.01675, 0.03268, -0.99933)79.19835, 39.32833, 62.95987

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Components

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


Mass: 22036.701 Da / Num. of mol.: 3 / Mutation: H135A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: PUC19 / Production host: Escherichia coli (E. coli) / References: UniProt: P06886
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 3.57 Å3/Da / Density % sol: 60 %
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 4.6 / Method: vapor diffusion
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.UnitCommon nameCrystal-IDSol-IDChemical formula
30.65-0.85 M1reservoirLiCl
4100 mM1reservoirNHOAc
50.02 %1reservoirNaN3
1mg/mlmutant toxin solution1drop
2%PEG40001reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.94
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 24, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionNum. obs: 30013 / % possible obs: 90.3 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.081
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.251 / % possible all: 92.2
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Num. measured all: 179091
Reflection shell
*PLUS
% possible obs: 92.2 % / Mean I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.5→10 Å / σ(F): 0
RfactorNum. reflection
Rfree0.275 -
Rwork0.202 -
obs0.202 29485
Displacement parametersBiso mean: 19.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4662 0 0 123 4785
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_deg1.69
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.96
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 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 29485 / Num. reflection obs: 26854 / Rfactor all: 0.202 / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.96

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