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- PDB-1eu3: CRYSTAL STRUCTURE OF THE SUPERANTIGEN SMEZ-2 (ZINC BOUND) FROM ST... -

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Basic information

Entry
Database: PDB / ID: 1eu3
TitleCRYSTAL STRUCTURE OF THE SUPERANTIGEN SMEZ-2 (ZINC BOUND) 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 enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / 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 enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / 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
: / PHOSPHATE ION / Mitogenic exotoxin Z 2
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.68 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 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,8918
Polymers48,4362
Non-polymers4556
Water7,494416
1
A: SUPERANTIGEN SMEZ-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3233
Polymers24,2181
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SUPERANTIGEN SMEZ-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5685
Polymers24,2181
Non-polymers3504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.230, 39.960, 104.070
Angle α, β, γ (deg.)90.00, 134.05, 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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: PEG 5000 MME, cacodylate, sodium phosphate, Zinc acetate, 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: Feb 28, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.68→40 Å / Num. all: 275416 / Num. obs: 275416 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 38.1
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.231 / Num. unique all: 4742 / % possible all: 94.7
Reflection
*PLUS
Num. obs: 49704 / % possible obs: 95.4 % / Num. measured all: 537930 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 84.7 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 6.2

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.68→37.05 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 527066.93 / 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
Rfree0.23 9123 9.8 %RANDOM
Rwork0.207 ---
obs0.207 93448 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.96 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 17.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å21.32 Å2
2---0.41 Å20 Å2
3----0.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-40 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.68→37.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3416 0 18 416 3850
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it0.671.5
X-RAY DIFFRACTIONc_mcangle_it1.152
X-RAY DIFFRACTIONc_scbond_it0.922
X-RAY DIFFRACTIONc_scangle_it1.412.5
LS refinement shellResolution: 1.68→1.74 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.37 836 10.1 %
Rwork0.341 7475 -
obs--84.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.8 % / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.37 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.341

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