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- PDB-8u5d: Crystal Structure of C-terminal domain of Clostridium perfringens... -

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Basic information

Entry
Database: PDB / ID: 8u5d
TitleCrystal Structure of C-terminal domain of Clostridium perfringens Enterotoxin in Space Group P 41 21 2
ComponentsHeat-labile enterotoxin B chain
KeywordsTOXIN / HEAT-LABILE ENTEROTOXIN
Function / homologyClostridium enterotoxin / Clostridium enterotoxin / toxin activity / extracellular region / ACETATE ION / Heat-labile enterotoxin B chain
Function and homology information
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKapoor, S. / Vecchio, A.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM138368 United States
CitationJournal: Toxins / Year: 2023
Title: Structural Basis of Clostridium perfringens Enterotoxin Activation and Oligomerization by Trypsin.
Authors: Ogbu, C.P. / Kapoor, S. / Vecchio, A.J.
History
DepositionSep 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat-labile enterotoxin B chain
B: Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,77232
Polymers31,3692
Non-polymers2,40330
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.120, 65.120, 130.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Heat-labile enterotoxin B chain


Mass: 15684.372 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: cpe / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01558
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.37 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100 mM sodium acetate pH 4.5, 200 mM sodium chloride, and 1.3 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.6→19.7 Å / Num. obs: 70024 / % possible obs: 99.52 % / Redundancy: 1.73 % / Biso Wilson estimate: 39.63 Å2 / CC1/2: 0.9952 / Net I/σ(I): 10.8
Reflection shellResolution: 1.6→1.657 Å / Mean I/σ(I) obs: 0.42 / Num. unique obs: 5197 / CC1/2: 0.127

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDS0.82data reduction
pointlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→19.7 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2226 3735 5.34 %
Rwork0.196 --
obs0.1975 69964 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 157 136 2242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142208
X-RAY DIFFRACTIONf_angle_d1.2482982
X-RAY DIFFRACTIONf_dihedral_angle_d12.6351300
X-RAY DIFFRACTIONf_chiral_restr0.082319
X-RAY DIFFRACTIONf_plane_restr0.006380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62030.41271410.40242480X-RAY DIFFRACTION99
1.6203-1.64160.40671370.38652449X-RAY DIFFRACTION99
1.6416-1.66410.38811400.37512483X-RAY DIFFRACTION99
1.6641-1.68780.41961380.36292471X-RAY DIFFRACTION99
1.6878-1.7130.4311420.35762464X-RAY DIFFRACTION99
1.713-1.73980.38721380.34912459X-RAY DIFFRACTION99
1.7398-1.76830.37071340.32472440X-RAY DIFFRACTION98
1.7683-1.79870.38331400.30422448X-RAY DIFFRACTION98
1.7987-1.83140.3231390.28962431X-RAY DIFFRACTION99
1.8314-1.86660.29941390.27172508X-RAY DIFFRACTION99
1.8666-1.90470.27181390.2592447X-RAY DIFFRACTION99
1.9047-1.94610.27391320.24782466X-RAY DIFFRACTION99
1.9461-1.99130.26351370.23352447X-RAY DIFFRACTION99
1.9913-2.04110.29771430.22262475X-RAY DIFFRACTION99
2.0411-2.09620.26581350.21632440X-RAY DIFFRACTION98
2.0962-2.15780.23351360.19362455X-RAY DIFFRACTION99
2.1578-2.22730.2491390.18942454X-RAY DIFFRACTION99
2.2273-2.30680.21461400.18642465X-RAY DIFFRACTION99
2.3068-2.39910.23751430.18512455X-RAY DIFFRACTION99
2.3991-2.5080.20141380.18722484X-RAY DIFFRACTION99
2.508-2.640.22941440.17482451X-RAY DIFFRACTION99
2.64-2.80490.19961370.16512459X-RAY DIFFRACTION99
2.8049-3.02080.20051390.17032434X-RAY DIFFRACTION98
3.0208-3.32350.21041410.16272445X-RAY DIFFRACTION98
3.3235-3.80140.15781350.1622405X-RAY DIFFRACTION97
3.8014-4.77810.21451360.15732430X-RAY DIFFRACTION98
4.7781-19.70.17281330.20542384X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.7480.6166-0.90673.8029-1.29053.87420.05510.01290.23520.01530.08-0.0363-0.21830.1761-0.1330.1548-0.01650.03490.1793-0.0440.2181-6.645216.3827-1.6033
21.5357-0.0901-0.19642.60391.5125.7110.03040.019-0.04350.04380.0480.04910.3704-0.0702-0.07350.1610.0085-0.010.1952-0.01450.2078-20.7338-1.7389-14.6078
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 13:129)
2X-RAY DIFFRACTION2(chain B and resseq 3:129)

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