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- PDB-8gw2: Escherichia Coli Heat Labile Enterotoxin Type IIB B-Pentamer Circ... -

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Basic information

Entry
Database: PDB / ID: 8gw2
TitleEscherichia Coli Heat Labile Enterotoxin Type IIB B-Pentamer Circular Permutant CP13-14
ComponentsHeat-labile enterotoxin IIB, B chain
KeywordsTOXIN / E. coli / LTIIB / LT-IIb-B5 / adjuvant / Toll-like receptor binding / TLR2/TLR1 signaling pathway / GD1a binding / ganglioside binding / circular permutation
Function / homologyType II heat-labile enterotoxin, B subunit / Type II heat-labile enterotoxin, B subunit superfamily / Type II heat-labile enterotoxin , B subunit (LT-IIB) / Enterotoxin / host cell membrane / toxin activity / extracellular region / Heat-labile enterotoxin IIB, B chain
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsHsu, S.H. / Yuan, Y.T. / Sue, S.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: To Be Published
Title: Escherichia Coli Heat Labile Enterotoxin Type IIB B-Pentamer Circular Permutant (CP13-14)
Authors: Hsu, S.H. / Yuan, Y.T. / Sue, S.C.
History
DepositionSep 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Heat-labile enterotoxin IIB, B chain
A: Heat-labile enterotoxin IIB, B chain
B: Heat-labile enterotoxin IIB, B chain
C: Heat-labile enterotoxin IIB, B chain
E: Heat-labile enterotoxin IIB, B chain


Theoretical massNumber of molelcules
Total (without water)55,3325
Polymers55,3325
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-94 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.430, 69.540, 107.484
Angle α, β, γ (deg.)90.000, 106.400, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Heat-labile enterotoxin IIB, B chain / LT-IIB


Mass: 11066.447 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P43529
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M sodium citrate pH 6, 0.1 M MgCl2, 15% v/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.71→30 Å / Num. obs: 13510 / % possible obs: 98.48 % / Redundancy: 2.8 % / Biso Wilson estimate: 40.66 Å2 / CC1/2: 0.84 / Rrim(I) all: 0.14 / Net I/σ(I): 12.1
Reflection shellResolution: 2.71→2.8 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1289 / Rrim(I) all: 0.64 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QB5

1qb5


Resolution: 2.71→25.78 Å / SU ML: 0.424 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.2647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2984 1366 10.11 %
Rwork0.2061 12144 -
obs0.215 13510 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.09 Å2
Refinement stepCycle: LAST / Resolution: 2.71→25.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3845 0 0 47 3892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00833900
X-RAY DIFFRACTIONf_angle_d1.0155275
X-RAY DIFFRACTIONf_chiral_restr0.0578600
X-RAY DIFFRACTIONf_plane_restr0.0081685
X-RAY DIFFRACTIONf_dihedral_angle_d6.9847550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.80.41621340.29991128X-RAY DIFFRACTION93.69
2.8-2.910.37331400.2761232X-RAY DIFFRACTION98.92
2.91-3.050.35781240.2451210X-RAY DIFFRACTION99.26
3.05-3.210.40551370.25111212X-RAY DIFFRACTION99.48
3.21-3.410.35751410.22061203X-RAY DIFFRACTION99.33
3.41-3.670.30931460.20771230X-RAY DIFFRACTION99.14
3.67-4.040.26171360.19411220X-RAY DIFFRACTION99.34
4.04-4.620.2421330.16361236X-RAY DIFFRACTION98.63
4.62-5.810.2551320.17981234X-RAY DIFFRACTION98.7
5.81-25.780.25011430.18781239X-RAY DIFFRACTION97.46

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