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- PDB-8u5e: Crystal Structure of C-terminal domain of Clostridium perfringens... -

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Basic information

Entry
Database: PDB / ID: 8u5e
TitleCrystal Structure of C-terminal domain of Clostridium perfringens Enterotoxin in Space Group P 21 21 21
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: 1.4 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
C: Heat-labile enterotoxin B chain
D: Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,48525
Polymers62,7374
Non-polymers1,74821
Water12,124673
1
A: Heat-labile enterotoxin B chain
B: Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,10211
Polymers31,3692
Non-polymers7349
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Heat-labile enterotoxin B chain
D: Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,38314
Polymers31,3692
Non-polymers1,01412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.630, 64.000, 136.980
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
Heat-labile enterotoxin B chain


Mass: 15684.372 Da / Num. of mol.: 4
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 673 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
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 1.0 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 20, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.4→59.187 Å / Num. obs: 186626 / % possible obs: 88.96 % / Redundancy: 2.19 % / CC1/2: 0.999 / Net I/σ(I): 9.55
Reflection shellResolution: 1.4→1.45 Å / Mean I/σ(I) obs: 0.29 / Num. unique obs: 5803 / CC1/2: 0.125

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDS0.82data reduction
pointlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→59.187 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2046 3571 1.94 %
Rwork0.1612 --
obs0.1621 183919 83.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→59.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 0 111 673 4774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034354
X-RAY DIFFRACTIONf_angle_d0.6425938
X-RAY DIFFRACTIONf_dihedral_angle_d16.0351590
X-RAY DIFFRACTIONf_chiral_restr0.073656
X-RAY DIFFRACTIONf_plane_restr0.003766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41850.4816380.43751955X-RAY DIFFRACTION24
1.4185-1.43790.3907430.43532350X-RAY DIFFRACTION28
1.4379-1.45840.4584510.40153256X-RAY DIFFRACTION39
1.4584-1.48020.4439750.38654057X-RAY DIFFRACTION49
1.4802-1.50330.3784870.36294859X-RAY DIFFRACTION59
1.5033-1.5280.4161040.34435530X-RAY DIFFRACTION66
1.528-1.55430.31571220.31186298X-RAY DIFFRACTION76
1.5543-1.58260.35771330.28246952X-RAY DIFFRACTION84
1.5826-1.6130.35461490.26757789X-RAY DIFFRACTION94
1.613-1.6460.29251700.25268205X-RAY DIFFRACTION99
1.646-1.68180.30231700.23888179X-RAY DIFFRACTION99
1.6818-1.72090.27871530.23298134X-RAY DIFFRACTION98
1.7209-1.76390.26681690.21958119X-RAY DIFFRACTION98
1.7639-1.81160.28521660.21237894X-RAY DIFFRACTION96
1.8116-1.86490.24921530.19438107X-RAY DIFFRACTION97
1.8649-1.92510.2271700.16788172X-RAY DIFFRACTION99
1.9251-1.99390.20211650.15668209X-RAY DIFFRACTION99
1.9939-2.07380.20631650.15128057X-RAY DIFFRACTION98
2.0738-2.16820.21011550.14827919X-RAY DIFFRACTION96
2.1682-2.28250.22541620.15078164X-RAY DIFFRACTION98
2.2825-2.42550.21171690.1498144X-RAY DIFFRACTION98
2.4255-2.61280.23741630.15138094X-RAY DIFFRACTION98
2.6128-2.87570.21521570.14877875X-RAY DIFFRACTION95
2.8757-3.29180.16941670.13458136X-RAY DIFFRACTION98
3.2918-4.14710.13141590.11897883X-RAY DIFFRACTION95
4.1471-59.1870.15631560.13588011X-RAY DIFFRACTION97

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