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

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Basic information

Entry
Database: PDB / ID: 4rgm
TitleStructure of Staphylococcal Enterotoxin B bound to the neutralizing antibody 20B1
Components
  • 20B1 heavy chain
  • 20B1 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 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 enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / 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 / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.689 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 / 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 1.4Oct 30, 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
S: Enterotoxin type B
L: 20B1 light chain
H: 20B1 heavy chain
A: Enterotoxin type B
B: 20B1 light chain
C: 20B1 heavy chain


Theoretical massNumber of molelcules
Total (without water)153,8426
Polymers153,8426
Non-polymers00
Water2,630146
1
S: Enterotoxin type B
L: 20B1 light chain
H: 20B1 heavy chain


Theoretical massNumber of molelcules
Total (without water)76,9213
Polymers76,9213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-35 kcal/mol
Surface area29730 Å2
MethodPISA
2
A: Enterotoxin type B
B: 20B1 light chain
C: 20B1 heavy chain


Theoretical massNumber of molelcules
Total (without water)76,9213
Polymers76,9213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-34 kcal/mol
Surface area29660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.467, 83.669, 174.731
Angle α, β, γ (deg.)90.00, 91.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11S
21A
12L
22B
13H
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114S1 - 237
2114A1 - 237
1124L1 - 213
2124B1 - 213
1134H1 - 221
2134C1 - 221

NCS ensembles :
ID
1
2
3
DetailsThe pharmacologically relevant complex contains one 20B1 Fab and one SEB monomer. There are two such complexes in the asymmetric unit of the crystal, one containing chains S,L,H; the other containing chains A,B,C.

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Components

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


Mass: 28975.607 Da / Num. of mol.: 2 / 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 20B1 light chain


Mass: 23818.186 Da / Num. of mol.: 2 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma
#3: Antibody 20B1 heavy chain


Mass: 24127.199 Da / Num. of mol.: 2 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.69 Å3/Da / Density % sol: 54.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES sodium, pH 7.5, 20% w/v PEG8000, 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: Apr 29, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.689→174.679 Å / Num. all: 44051 / Num. obs: 43919 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 16.1
Reflection shellResolution: 2.689→2.75 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.5 / % possible all: 95.8

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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 AND 1JHK

1se4

1jhk


Resolution: 2.689→174.679 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.878 / SU B: 29.629 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27656 2194 5 %RANDOM
Rwork0.22514 ---
obs0.22777 43728 96.12 %-
all-45493 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.005 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å2-0.11 Å2
2--1.06 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.689→174.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10380 0 0 146 10526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02210638
X-RAY DIFFRACTIONr_bond_other_d0.0010.027199
X-RAY DIFFRACTIONr_angle_refined_deg1.0541.95114423
X-RAY DIFFRACTIONr_angle_other_deg0.765317575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99551296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19724.5480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.266151809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2791544
X-RAY DIFFRACTIONr_chiral_restr0.0640.21563
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111756
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022154
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_it0.2391.56501
X-RAY DIFFRACTIONr_mcbond_other0.0431.52625
X-RAY DIFFRACTIONr_mcangle_it0.469210550
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.70334137
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.1664.53873
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1S3175MEDIUM POSITIONAL0.320.5
1S3175MEDIUM THERMAL0.22
2L2818MEDIUM POSITIONAL0.410.5
2L2818MEDIUM THERMAL0.162
3H2775MEDIUM POSITIONAL0.320.5
3H2775MEDIUM THERMAL0.162
LS refinement shellResolution: 2.689→2.759 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 97 -
Rwork0.315 1633 -
obs--52.49 %
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)
11.0880.7655-0.49712.7187-0.72923.6531-0.005-0.02-0.00880.1302-0.0237-0.0752-0.14330.08350.02870.10310.0439-0.06090.039-0.01590.13124.1895-2.7773-3.04
23.4301-1.15810.5882.68410.20861.34160.03330.0529-0.0874-0.0644-0.00260.05070.0495-0.0025-0.03080.1129-0.0471-0.01880.03970.02220.0272-25.7203-71.1762-82.3069
32.8345-0.07831.16722.21823.60666.53560.04790.3705-0.1682-0.19450.04060.0022-0.18640.3108-0.08860.1660.0754-0.00440.2430.02990.157921.6952-16.6-42.4848
45.84512.7552.02131.93040.63125.12640.0611-0.06710.00230.2189-0.0962-0.3267-0.24040.50730.03520.1208-0.0073-0.05440.16590.03660.20026.3959-57.3218-59.3791
57.1827-3.35641.63933.5565-0.94322.6984-0.3857-0.45290.04220.0370.40050.0387-0.1723-0.096-0.01490.24380.0032-0.00940.21430.00460.1361-6.9581-14.5008-64.8188
64.09840.5542-3.1893.3244-3.27199.501-0.1322-0.3093-0.43990.09630.05890.06470.38220.76820.07330.1630.0425-0.06840.27610.01760.308211.085-59.4899-22.841
75.7998-1.4642.19262.28190.66853.69910.01030.11130.1588-0.0437-0.12570.14110.0397-0.44750.11540.0962-0.01510.00660.1902-0.03280.13026.157-13.2014-27.3147
82.04930.57170.34761.7492-0.03587.3657-0.0153-0.24070.05650.1679-0.15360.04780.2727-0.24810.16890.1054-0.03550.0280.1358-0.03020.1369-14.4994-61.0856-53.8438
93.8461-0.5366-0.28115.11073.79688.1078-0.1189-0.2033-0.3271-0.14120.05310.21020.1441-0.33230.06580.16010.05230.00070.2950.10720.283-13.0745-26.4359-55.6085
107.28980.70860.02923.9930.34065.1935-0.0241-0.21090.05590.3838-0.0039-0.1954-0.26530.18770.0280.24290.00660.01720.13620.02880.1239-0.366-48.0501-22.279
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1S2 - 237
2X-RAY DIFFRACTION2A2 - 237
3X-RAY DIFFRACTION3L1 - 108
4X-RAY DIFFRACTION4B1 - 108
5X-RAY DIFFRACTION5L109 - 213
6X-RAY DIFFRACTION6B109 - 213
7X-RAY DIFFRACTION7H1 - 120
8X-RAY DIFFRACTION8C1 - 120
9X-RAY DIFFRACTION9H121 - 222
10X-RAY DIFFRACTION10C121 - 221

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