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- PDB-1aw7: Q136A MUTANT OF TOXIC SHOCK SYNDROME TOXIN-1 FROM S. AUREUS -

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Basic information

Entry
Database: PDB / ID: 1aw7
TitleQ136A 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: 1.95 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 11, 1997Processing site: BNL
Revision 1.0Oct 28, 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 2, 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
C: TOXIC SHOCK SYNDROME TOXIN-1
D: TOXIC SHOCK SYNDROME TOXIN-1


Theoretical massNumber of molelcules
Total (without water)88,1874
Polymers88,1874
Non-polymers00
Water5,242291
1
A: TOXIC SHOCK SYNDROME TOXIN-1


Theoretical massNumber of molelcules
Total (without water)22,0471
Polymers22,0471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TOXIC SHOCK SYNDROME TOXIN-1


Theoretical massNumber of molelcules
Total (without water)22,0471
Polymers22,0471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TOXIC SHOCK SYNDROME TOXIN-1


Theoretical massNumber of molelcules
Total (without water)22,0471
Polymers22,0471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: TOXIC SHOCK SYNDROME TOXIN-1


Theoretical massNumber of molelcules
Total (without water)22,0471
Polymers22,0471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.630, 99.280, 41.330
Angle α, β, γ (deg.)88.50, 93.30, 91.10
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99221, 0.00089, -0.12457), (-0.00808, -0.99833, 0.05722), (-0.12431, 0.05778, 0.99056)18.422, 13.979, 0.792
2given(0.98624, -0.11587, 0.11791), (-0.11638, -0.9932, -0.0026), (0.11741, -0.01116, -0.99302)24.369, 64.784, 4.587
3given(-0.99289, 0.11775, -0.01727), (0.11843, 0.99191, -0.04579), (0.01174, -0.04751, -0.9988)41.003, 48.804, 5.888

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Components

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


Mass: 22046.719 Da / Num. of mol.: 4
Mutation: CHAIN A, Q136A, CHAIN B, Q336A, CHAIN C, Q536A, CHAIN D, Q736A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / References: UniProt: P06886
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
28-22 %PEG40001reservoir
35-15 %2-propanol1reservoir
4100 mMHEPES1reservoir

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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: Nov 1, 1996
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 38992 / % possible obs: 79 % / Redundancy: 3.1 % / Rsym value: 0.056 / Net I/σ(I): 12.7
Reflection shellResolution: 1.95→2.01 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 1 / Rsym value: 0.24 / % possible all: 37
Reflection
*PLUS
Highest resolution: 1.95 Å / Num. obs: 50028 / Num. measured all: 157168 / Rmerge(I) obs: 0.056

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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: 1.95→20 Å / Data cutoff high absF: 100000000 / Data cutoff low absF: 0 / σ(F): 0 /
RfactorNum. reflection
Rwork0.176 -
obs0.176 46153
Displacement parametersBiso mean: 25.27 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6248 0 0 291 6539
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_it2.581.5
X-RAY DIFFRACTIONx_mcangle_it3.862
X-RAY DIFFRACTIONx_scbond_it3.832
X-RAY DIFFRACTIONx_scangle_it5.62.5
LS refinement shellResolution: 1.95→1.98 Å / Rfactor Rwork: 0.319 / Total num. of bins used: 20

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