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- PDB-8h2r: Escherichia Coli Heat Labile Enterotoxin Type IIB B-Pentamer Circ... -

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Basic information

Entry
Database: PDB / ID: 8h2r
TitleEscherichia Coli Heat Labile Enterotoxin Type IIB B-Pentamer Circular Permutant CP52-53
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: 2.9 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 CP52-53
Authors: Hsu, S.H. / Yuan, Y.T. / Sue, S.C.
History
DepositionOct 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 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
A: Heat-labile enterotoxin IIB, B chain
B: Heat-labile enterotoxin IIB, B chain
C: Heat-labile enterotoxin IIB, B chain
D: 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
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11700 Å2
ΔGint-85 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.385, 69.789, 88.338
Angle α, β, γ (deg.)90.000, 114.490, 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: 11066.451 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
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: 45.3 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M sodium citrate pH 5, 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: BL13B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 7547 / % possible obs: 97.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 49.82 Å2 / CC1/2: 0.87 / Rrim(I) all: 0.14 / Net I/σ(I): 8.1
Reflection shellResolution: 2.9→3 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 7546 / Rrim(I) all: 0.63

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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: 2.9→26.8 Å / SU ML: 0.4918 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.4411
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3498 744 9.89 %
Rwork0.225 6782 -
obs0.2373 7526 81.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.55 Å2
Refinement stepCycle: LAST / Resolution: 2.9→26.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3845 0 0 0 3845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00943900
X-RAY DIFFRACTIONf_angle_d1.2315275
X-RAY DIFFRACTIONf_chiral_restr0.0585600
X-RAY DIFFRACTIONf_plane_restr0.009685
X-RAY DIFFRACTIONf_dihedral_angle_d8.7075550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.120.3895910.2326833X-RAY DIFFRACTION50.19
3.12-3.440.36441270.24241187X-RAY DIFFRACTION71.34
3.44-3.930.36981620.25221474X-RAY DIFFRACTION89.59
3.93-4.950.33611830.19521633X-RAY DIFFRACTION98.32
4.95-26.80.33751810.22981655X-RAY DIFFRACTION97.61

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