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- PDB-4rgo: Structure of Staphylococcal Enterotoxin B bound to the neutralizi... -

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Basic information

Entry
Database: PDB / ID: 4rgo
TitleStructure of Staphylococcal Enterotoxin B bound to the neutralizing antibody 14G8
Components
  • 14G8 heavy chain
  • 14G8 light chain
  • Enterotoxin type B
KeywordsTOXIN/IMMUNE SYSTEM / Neutralizing antibody / Staphylococcal enterotoxin B / TOXIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


toxin activity / extracellular region / metal ion binding
Similarity search - Function
Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / 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 ...Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / 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) / Immunoglobulins / Roll / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Enterotoxin type B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFranklin, M.C. / Dutta, K. / Varshney, A.K. / Goger, M.J. / Fries, B.C.
Citation
Journal: J.Biol.Chem. / Year: 2015
Title: Mechanisms mediating enhanced neutralization efficacy of staphylococcal enterotoxin B by combinations of monoclonal antibodies.
Authors: Dutta, K. / Varshney, A.K. / Franklin, M.C. / Goger, M. / Wang, X. / Fries, B.C.
#1: Journal: J.Biol.Chem. / Year: 2011
Title: Generation, characterization, and epitope mapping of neutralizing and protective monoclonal antibodies against staphylococcal enterotoxin B-induced lethal shock.
Authors: Varshney, A.K. / Wang, X. / Cook, E. / Dutta, K. / Scharff, M.D. / Goger, M.J. / Fries, B.C.
History
DepositionSep 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Apr 1, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
S: Enterotoxin type B
H: 14G8 heavy chain
L: 14G8 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4084
Polymers76,3493
Non-polymers591
Water16,358908
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.576, 85.292, 115.017
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe pharmacologically relevant complex contains one 14G8 Fab and one SEB monomer. There is one such complex in the asymmetric unit of the crystal.

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Components

#1: Protein Enterotoxin type B / SEB / Staphylococcal enterotoxin B


Mass: 28975.607 Da / Num. of mol.: 1 / Fragment: UNP residues 28-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: entB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01552
#2: Antibody 14G8 heavy chain


Mass: 23783.713 Da / Num. of mol.: 1 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma
#3: Antibody 14G8 light chain


Mass: 23589.906 Da / Num. of mol.: 1 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 908 / 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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 80 mM sodium cacodylate, pH 6.5, 16% w/v PEG8000, 160 mM magnesium acetate, 20% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 14, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 77677 / Num. obs: 77133 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 38.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.8 / % possible all: 89.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1SE4, 3FFD, AND 3D9A

1se4

3ffd

3d9a


Resolution: 1.8→42.65 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.901 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18903 3830 5 %RANDOM
Rwork0.14195 ---
obs0.14433 76413 98.41 %-
all-77647 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.132 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--1.6 Å20 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5140 0 4 908 6052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225334
X-RAY DIFFRACTIONr_bond_other_d0.0010.023598
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9557256
X-RAY DIFFRACTIONr_angle_other_deg0.83538801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.224.304237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24515898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.851523
X-RAY DIFFRACTIONr_chiral_restr0.0860.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215931
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021087
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9741.53272
X-RAY DIFFRACTIONr_mcbond_other0.2971.51321
X-RAY DIFFRACTIONr_mcangle_it1.61925325
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.74632062
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0554.51919
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.12738932
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 267 -
Rwork0.272 4877 -
obs--90.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.22290.69560.59522.95361.07661.79790.02920.1154-0.1196-0.13550.0544-0.0931-0.02180.1416-0.08350.02150.016-0.01440.07730.00370.0686-22.321766.2113-68.8028
22.68481.04141.00552.68761.21023.10620.0168-0.00620.0763-0.09550.0254-0.1354-0.12290.0613-0.04220.0469-0.01280.02180.01030.00460.0353-6.415987.4317-41.4509
31.71750.1862-0.28685.7872-2.61673.99-0.099-0.0387-0.09910.0338-0.0705-0.32260.29990.57780.16950.12730.07330.00530.243-0.03650.13466.716480.1356-14.2871
41.79630.43380.32931.9096-1.07945.26940.0485-0.1391-0.17550.2059-0.04160.13280.3295-0.4828-0.00690.1129-0.09670.02280.1458-0.02650.0608-22.651575.8589-32.8821
52.28751.34910.75053.02210.96244.20130.0294-0.2817-0.00380.17820.0064-0.11720.21810.2226-0.03580.10590.0497-0.00580.12040.00770.0808-4.431681.0903-1.6365
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1S2 - 238
2X-RAY DIFFRACTION2H1 - 119
3X-RAY DIFFRACTION3H120 - 220
4X-RAY DIFFRACTION4L1 - 107
5X-RAY DIFFRACTION5L108 - 212

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