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- PDB-8ybl: Crystal structure of nanobody SEB-Nb3 bound to staphylococcal ent... -

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Basic information

Entry
Database: PDB / ID: 8ybl
TitleCrystal structure of nanobody SEB-Nb3 bound to staphylococcal enterotoxin B (SEB)
Components
  • Enterotoxin type B
  • nanobody SEB-Nb3
KeywordsANTITOXIN / antibody / nanobody / toxin / staphylococcal enterotoxin B (SEB)
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. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Superantigen toxin, C-terminal / Enterotoxin
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsDing, Y. / Zong, X. / Liu, R. / Liu, P.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA0805200 China
National Natural Science Foundation of China (NSFC)32070939 China
National Natural Science Foundation of China (NSFC)82030106 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural insights into the binding of nanobodies to the Staphylococcal enterotoxin B.
Authors: Zong, X. / Liu, P. / Wang, Z. / Zhu, H. / Zhong, C. / Zhong, P. / Jiang, H. / Liu, J. / Ma, Z. / Liu, X. / Liu, R. / Ding, Y.
History
DepositionFeb 15, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enterotoxin type B
B: nanobody SEB-Nb3


Theoretical massNumber of molelcules
Total (without water)42,5332
Polymers42,5332
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, isothermal titration calorimetry, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-7 kcal/mol
Surface area16620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.570, 83.751, 86.972
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Enterotoxin type B


Mass: 28542.262 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 nanobody SEB-Nb3


Mass: 13990.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 8% v/v Tacsimate pH 5.0, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.33→60.33 Å / Num. obs: 18666 / % possible obs: 100 % / Redundancy: 6.2 % / CC1/2: 0.982 / Rmerge(I) obs: 0.284 / Rpim(I) all: 0.123 / Rrim(I) all: 0.31 / Χ2: 0.96 / Net I/σ(I): 5.4 / Num. measured all: 115931
Reflection shellResolution: 2.33→2.45 Å / % possible obs: 100 % / Redundancy: 5.8 % / Rmerge(I) obs: 1.378 / Num. measured all: 15453 / Num. unique obs: 2664 / CC1/2: 0.46 / Rpim(I) all: 0.627 / Rrim(I) all: 1.518 / Χ2: 0.91 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimless0.7.7data scaling
XDSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→60.33 Å / SU B: 20.615 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.366 / ESU R Free: 0.251 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26163 906 4.9 %RANDOM
Rwork0.22317 ---
obs0.22506 17692 99.87 %-
Displacement parametersBiso mean: 12.969 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20 Å2
2--2.86 Å2-0 Å2
3----2.22 Å2
Refinement stepCycle: LAST / Resolution: 2.33→60.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2855 0 0 50 2905

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