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- PDB-3owe: Crystal Structure of Staphylococcal Enterotoxin G (SEG) in Comple... -

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Basic information

Entry
Database: PDB / ID: 3owe
TitleCrystal Structure of Staphylococcal Enterotoxin G (SEG) in Complex with a High Affinity Mutant Mouse T-cell Receptor Chain
Components
  • Beta-chain
  • Enterotoxin SEG
KeywordsIMMUNE SYSTEM / T-CELL RECEPTOR V BETA DOMAIN / COMPLEX STRUCTURE / IgG domains / B grasp / virulence factors
Function / homology
Function and homology information


T cell receptor complex / toxin activity / adaptive immune response / extracellular region
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. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain ...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. / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-chain / Enterotoxin SEG / Enterotoxin type Gv
Similarity search - Component
Biological speciesMus musculus (house mouse)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFernandez, M.M. / Cho, S. / Robinson, H. / Mariuzza, R.A. / Malchiodi, M.L.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal structure of staphylococcal enterotoxin G (SEG) in complex with a mouse T-cell receptor {beta} chain.
Authors: Fernandez, M.M. / Cho, S. / De Marzi, M.C. / Kerzic, M.C. / Robinson, H. / Mariuzza, R.A. / Malchiodi, E.L.
History
DepositionSep 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-chain
B: Enterotoxin SEG
C: Beta-chain
D: Enterotoxin SEG
E: Beta-chain
F: Enterotoxin SEG
G: Beta-chain
H: Enterotoxin SEG
I: Beta-chain
J: Enterotoxin SEG
K: Beta-chain
L: Enterotoxin SEG
M: Beta-chain
N: Enterotoxin SEG
O: Beta-chain
P: Enterotoxin SEG


Theoretical massNumber of molelcules
Total (without water)313,51216
Polymers313,51216
Non-polymers00
Water3,261181
1
A: Beta-chain
B: Enterotoxin SEG


Theoretical massNumber of molelcules
Total (without water)39,1892
Polymers39,1892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Beta-chain
D: Enterotoxin SEG


Theoretical massNumber of molelcules
Total (without water)39,1892
Polymers39,1892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Beta-chain
F: Enterotoxin SEG


Theoretical massNumber of molelcules
Total (without water)39,1892
Polymers39,1892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Beta-chain
H: Enterotoxin SEG


Theoretical massNumber of molelcules
Total (without water)39,1892
Polymers39,1892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Beta-chain
J: Enterotoxin SEG


Theoretical massNumber of molelcules
Total (without water)39,1892
Polymers39,1892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Beta-chain
L: Enterotoxin SEG


Theoretical massNumber of molelcules
Total (without water)39,1892
Polymers39,1892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: Beta-chain
N: Enterotoxin SEG


Theoretical massNumber of molelcules
Total (without water)39,1892
Polymers39,1892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
O: Beta-chain
P: Enterotoxin SEG


Theoretical massNumber of molelcules
Total (without water)39,1892
Polymers39,1892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.205, 141.205, 255.751
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Beta-chain


Mass: 12100.324 Da / Num. of mol.: 8 / Fragment: VARIABLE DOMAIN
Mutation: G17E, A52V, S54N, K66E, Q72H, E80V, L81S, T87S, G96V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A2NTY6
#2: Protein
Enterotoxin SEG


Mass: 27088.725 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pET 22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (D13) / References: UniProt: D0EMB6, UniProt: Q9ZNF2*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.06 Å3/Da / Density % sol: 69.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium citrate, 30% iso-propanol and 0.1 M sodium cacodylate, Protein concentration: 3.25 mg/ml in the drop, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.5

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2007
Details: Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 152700 / % possible obs: 75 % / Observed criterion σ(F): 2.046 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.111

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AQ3

2aq3


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.387 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 7666 5 %RANDOM
Rwork0.211 ---
obs-144940 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.069 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.32 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21499 0 0 181 21680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.02222011
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6631.95229748
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.47452651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.22124.7081043
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.026153782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5951580
X-RAY DIFFRACTIONr_chiral_restr0.180.23195
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216752
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2680.29443
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3370.215022
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.21035
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3040.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6531.513795
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.692221592
X-RAY DIFFRACTIONr_scbond_it3.83239625
X-RAY DIFFRACTIONr_scangle_it5.5134.58156
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 523 -
Rwork0.306 10462 -
obs--97.16 %

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