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- PDB-1et6: CRYSTAL STRUCTURE OF THE SUPERANTIGEN SMEZ-2 FROM STREPTOCOCCUS P... -

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Basic information

Entry
Database: PDB / ID: 1et6
TitleCRYSTAL STRUCTURE OF THE SUPERANTIGEN SMEZ-2 FROM STREPTOCOCCUS PYOGENES
ComponentsSUPERANTIGEN SMEZ-2
KeywordsIMMUNE SYSTEM / beta grasp / OB fold / superantigen fold
Function / homology
Function and homology information


toxin activity / extracellular region / metal ion binding
Similarity search - Function
Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal ...Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Ubiquitin-like (UB roll) - #120 / 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
Mitogenic exotoxin Z 2
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsArcus, V.L. / Proft, T. / Sigrell, J.A. / Baker, H.M. / Fraser, J.D. / Baker, E.N.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Conservation and variation in superantigen structure and activity highlighted by the three-dimensional structures of two new superantigens from Streptococcus pyogenes.
Authors: Arcus, V.L. / Proft, T. / Sigrell, J.A. / Baker, H.M. / Fraser, J.D. / Baker, E.N.
History
DepositionApr 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUPERANTIGEN SMEZ-2
B: SUPERANTIGEN SMEZ-2


Theoretical massNumber of molelcules
Total (without water)48,4362
Polymers48,4362
Non-polymers00
Water4,107228
1
A: SUPERANTIGEN SMEZ-2


Theoretical massNumber of molelcules
Total (without water)24,2181
Polymers24,2181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SUPERANTIGEN SMEZ-2


Theoretical massNumber of molelcules
Total (without water)24,2181
Polymers24,2181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.085, 39.935, 104.727
Angle α, β, γ (deg.)90.00, 134.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SUPERANTIGEN SMEZ-2


Mass: 24218.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: 2035 / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RQQ5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: PEG 5000 MME, cacodylate, sodium phosphate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
250 mMphosphate1drop
3200 mMcacodylate/KOH1reservoir
416 %PEG5000 MME1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 23, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 121290 / Num. obs: 121290 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 21.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.312 / Num. unique all: 3380 / % possible all: 98.5
Reflection
*PLUS
Num. obs: 34777 / % possible obs: 97 % / Num. measured all: 227174
Reflection shell
*PLUS
% possible obs: 89.9 % / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→18.15 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 390805.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: protein.top
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3382 10 %RANDOM
Rwork0.219 ---
obs0.221 33879 97 %-
all-33879 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.8857 Å2 / ksol: 0.343089 e/Å3
Displacement parametersBiso mean: 21.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å22.78 Å2
2---2.08 Å20 Å2
3---1.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-20 Å
Luzzati sigma a0.2 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→18.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 0 228 3508
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_mcangle_it1.582
X-RAY DIFFRACTIONc_scbond_it1.472
X-RAY DIFFRACTIONc_scangle_it2.152.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.337 301 9.8 %
Rwork0.313 2784 -
obs--89.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.66
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
X-RAY DIFFRACTIONc_bond_d0.006
LS refinement shell
*PLUS
Rfactor Rfree: 0.337 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.313

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