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- PDB-3w2d: Crystal Structure of Staphylococcal Eenterotoxin B in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3w2d
TitleCrystal Structure of Staphylococcal Eenterotoxin B in complex with a novel neutralization monoclonal antibody Fab fragment
Components
  • Enterotoxin type B
  • Monoclonal Antibody 3E2 Fab figment heavy chain
  • Monoclonal Antibody 3E2 Fab figment light chain
KeywordsIMMUNE SYSTEM / Staphylococcal Eenterotoxin B
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
Biological speciesStaphylococcus aureus (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLiang, S.Y. / Hu, S. / Dai, J.X. / Guo, Y.J. / Lou, Z.Y.
CitationJournal: MAbs / Year: 2014
Title: Structural basis for the neutralization and specificity of Staphylococcal enterotoxin B against its MHC Class II binding site.
Authors: Xia, T. / Liang, S. / Wang, H. / Hu, S. / Sun, Y. / Yu, X. / Han, J. / Li, J. / Guo, S. / Dai, J. / Lou, Z. / Guo, Y.
History
DepositionNov 28, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references / Source and taxonomy

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enterotoxin type B
L: Monoclonal Antibody 3E2 Fab figment light chain
H: Monoclonal Antibody 3E2 Fab figment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4114
Polymers76,3153
Non-polymers961
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-54 kcal/mol
Surface area29010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.561, 109.308, 86.222
Angle α, β, γ (deg.)90.00, 96.08, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11L-301-

HOH

21L-329-

HOH

31L-330-

HOH

41H-402-

HOH

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Components

#1: Protein Enterotoxin type B / SEB


Mass: 28411.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: entB / Production host: Escherichia coli (E. coli) / References: UniProt: P01552
#2: Antibody Monoclonal Antibody 3E2 Fab figment light chain


Mass: 23460.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Antibody Monoclonal Antibody 3E2 Fab figment heavy chain


Mass: 24443.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.49 Å3/Da / Density % sol: 50.61 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 13571 / % possible obs: 99.5 % / Observed criterion σ(F): 7.1 / Observed criterion σ(I): 3.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.1_743) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→36.436 Å / SU ML: 1.01 / σ(F): 1.36 / Phase error: 28.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2611 669 4.96 %
Rwork0.1963 --
obs0.1997 13478 98.82 %
all-13571 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.473 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.3756 Å2-0 Å27.9234 Å2
2--4.4509 Å20 Å2
3----8.8265 Å2
Refinement stepCycle: LAST / Resolution: 3.1→36.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5253 0 5 135 5393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115392
X-RAY DIFFRACTIONf_angle_d1.5357318
X-RAY DIFFRACTIONf_dihedral_angle_d18.9431953
X-RAY DIFFRACTIONf_chiral_restr0.106799
X-RAY DIFFRACTIONf_plane_restr0.006931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.33920.3731340.26022504X-RAY DIFFRACTION98
3.3392-3.6750.32411410.20072554X-RAY DIFFRACTION99
3.675-4.20610.22271240.17972532X-RAY DIFFRACTION99
4.2061-5.29660.21871290.15892596X-RAY DIFFRACTION99
5.2966-36.43850.24311410.21742623X-RAY DIFFRACTION100

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