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- PDB-8ybm: Crystal structure of nanobody SEB-Nb6 bound to staphylococcal ent... -

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Basic information

Entry
Database: PDB / ID: 8ybm
TitleCrystal structure of nanobody SEB-Nb6 bound to staphylococcal enterotoxin B (SEB)
Components
  • Enterotoxin type B
  • nanobody SEB-Nb6
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: 2.04 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
Revision 1.1Jan 1, 2025Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enterotoxin type B
B: nanobody SEB-Nb6
C: Enterotoxin type B
D: nanobody SEB-Nb6


Theoretical massNumber of molelcules
Total (without water)84,9354
Polymers84,9354
Non-polymers00
Water4,612256
1
A: Enterotoxin type B
B: nanobody SEB-Nb6


Theoretical massNumber of molelcules
Total (without water)42,4682
Polymers42,4682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Enterotoxin type B
D: nanobody SEB-Nb6


Theoretical massNumber of molelcules
Total (without water)42,4682
Polymers42,4682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.199, 85.588, 176.510
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.: 2
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-Nb6


Mass: 13925.297 Da / Num. of mol.: 2
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.: 256 / 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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 2% v/v 1,4-Dioxane, 0.1 M Tris pH 8.0, 15% 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: Sep 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.04→88.25 Å / Num. obs: 47585 / % possible obs: 99.8 % / Redundancy: 7.4 % / CC1/2: 0.983 / Rmerge(I) obs: 0.3 / Rpim(I) all: 0.12 / Rrim(I) all: 0.323 / Χ2: 0.95 / Net I/σ(I): 7.3 / Num. measured all: 352444
Reflection shellResolution: 2.04→2.15 Å / % possible obs: 99.5 % / Redundancy: 7.6 % / Rmerge(I) obs: 2.387 / Num. measured all: 51512 / Num. unique obs: 6805 / CC1/2: 0.363 / Rpim(I) all: 0.953 / Rrim(I) all: 2.574 / Χ2: 0.92 / 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: 2.04→88.25 Å / SU B: 13.351 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.194 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25891 2239 4.8 %RANDOM
Rwork0.21307 ---
obs0.21524 44856 98.76 %-
Displacement parametersBiso mean: 15.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2---1.56 Å20 Å2
3---1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.04→88.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5589 0 0 256 5845

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