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- PDB-8u5f: Crystal Structure of Trypsinized Clostridium perfringens Enterotoxin -

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Basic information

Entry
Database: PDB / ID: 8u5f
TitleCrystal Structure of Trypsinized Clostridium perfringens Enterotoxin
ComponentsHeat-labile enterotoxin B chain
KeywordsTOXIN / HEAT-LABILE ENTEROTOXIN
Function / homologyClostridium enterotoxin / Clostridium enterotoxin / toxin activity / extracellular region / PHOSPHATE ION / Heat-labile enterotoxin B chain
Function and homology information
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsKapoor, S. / Ogbu, C.P. / 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 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
E: Heat-labile enterotoxin B chain
F: Heat-labile enterotoxin B chain
G: Heat-labile enterotoxin B chain
H: Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,901118
Polymers305,2098
Non-polymers10,692110
Water6,575365
1
A: Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,00521
Polymers38,1511
Non-polymers1,85320
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,29223
Polymers38,1511
Non-polymers2,14122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,35114
Polymers38,1511
Non-polymers1,20013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,44315
Polymers38,1511
Non-polymers1,29214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,37612
Polymers38,1511
Non-polymers1,22511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,25913
Polymers38,1511
Non-polymers1,10812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,54915
Polymers38,1511
Non-polymers1,39814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6265
Polymers38,1511
Non-polymers4744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)200.330, 200.330, 254.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11D-549-

HOH

21D-556-

HOH

31F-526-

HOH

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Components

#1: Protein
Heat-labile enterotoxin B chain


Mass: 38151.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: cpe / Plasmid: pFastBac1 / Cell line (production host): Tn5 Expression Systems / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01558
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: PO4
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 89 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 4.19 Å3/Da / Density % sol: 70.63 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM potassium phosphate monobasic, 100 mM MES monohydrate pH 6.5, and 2.0 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.32→66.78 Å / Num. obs: 222147 / % possible obs: 99.62 % / Redundancy: 14.09 % / Biso Wilson estimate: 76.22 Å2 / CC1/2: 0.997 / Net I/σ(I): 7.17
Reflection shellResolution: 2.32→2.403 Å / Mean I/σ(I) obs: 0.39 / Num. unique obs: 16289 / CC1/2: 0.118

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDS0.82data reduction
pointlessdata scaling
MoRDaphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→66.777 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 1994 0.9 %
Rwork0.2239 --
obs0.2241 221336 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→66.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17805 0 674 365 18844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00218751
X-RAY DIFFRACTIONf_angle_d0.55325335
X-RAY DIFFRACTIONf_dihedral_angle_d11.09110925
X-RAY DIFFRACTIONf_chiral_restr0.0432813
X-RAY DIFFRACTIONf_plane_restr0.0033160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.3780.38611370.379715044X-RAY DIFFRACTION97
2.378-2.44230.36741420.367915449X-RAY DIFFRACTION99
2.4423-2.51420.39671410.349815534X-RAY DIFFRACTION100
2.5142-2.59540.37651420.327215591X-RAY DIFFRACTION100
2.5954-2.68810.30861400.301415553X-RAY DIFFRACTION100
2.6881-2.79580.31931430.290615635X-RAY DIFFRACTION100
2.7958-2.9230.28531410.281715626X-RAY DIFFRACTION100
2.923-3.07710.3681430.279715651X-RAY DIFFRACTION100
3.0771-3.26990.28741430.258215673X-RAY DIFFRACTION100
3.2699-3.52240.24811420.221715699X-RAY DIFFRACTION100
3.5224-3.87680.241430.209515750X-RAY DIFFRACTION100
3.8768-4.43770.22561440.183615852X-RAY DIFFRACTION100
4.4377-5.59060.17081460.178415944X-RAY DIFFRACTION100
5.5906-66.7770.2241470.201716341X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -31.0769 Å / Origin y: 76.0069 Å / Origin z: 25.8684 Å
111213212223313233
T0.4883 Å2-0.013 Å20.03 Å2-0.5493 Å20.0346 Å2--0.4566 Å2
L0.1519 °2-0.1146 °20.006 °2-0.25 °20.0765 °2--0.0043 °2
S-0.009 Å °0.0671 Å °-0.0426 Å °-0.0196 Å °0.0174 Å °-0.0442 Å °-0.006 Å °0.001 Å °-0.0047 Å °
Refinement TLS groupSelection details: all

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