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- PDB-7ee6: Crystal structure of PltC toxin -

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Basic information

Entry
Database: PDB / ID: 7ee6
TitleCrystal structure of PltC toxin
Components
  • Cytolethal distending toxin subunit B family protein
  • Pertussis-like toxin subunit ArtA
  • Subtilase cytotoxin subunit B-like protein
KeywordsTOXIN / typhoid toxin
Function / homology
Function and homology information


NAD+ ADP-ribosyltransferase activity / catalytic activity / extracellular region
Similarity search - Function
Cytolethal distending toxin B / Bordetella pertussis toxin A / Pertussis toxin, subunit 1 / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Enterotoxin / Endonuclease/exonuclease/phosphatase superfamily
Similarity search - Domain/homology
ACETONE / CITRATE ANION / DI(HYDROXYETHYL)ETHER / Pertussis-like toxin subunit ArtA / Subtilase cytotoxin subunit B-like protein / Cytolethal distending toxin subunit B family protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsLiu, X.Y. / Chen, Z. / Gao, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770143 China
CitationJournal: Mbio / Year: 2022
Title: Molecular Insights into the Assembly and Functional Diversification of Typhoid Toxin.
Authors: Liu, X. / Chen, Z. / Jiao, X. / Jiang, X. / Qiu, J. / You, F. / Long, H. / Cao, H. / Fowler, C.C. / Gao, X.
History
DepositionMar 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Subtilase cytotoxin subunit B-like protein
B: Subtilase cytotoxin subunit B-like protein
C: Subtilase cytotoxin subunit B-like protein
D: Subtilase cytotoxin subunit B-like protein
E: Subtilase cytotoxin subunit B-like protein
F: Cytolethal distending toxin subunit B family protein
G: Pertussis-like toxin subunit ArtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,57644
Polymers119,3797
Non-polymers3,19837
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24050 Å2
ΔGint-15 kcal/mol
Surface area38880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.997, 184.170, 68.838
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 3 types, 7 molecules ABCDEFG

#1: Protein
Subtilase cytotoxin subunit B-like protein / PltB homolog protein


Mass: 13413.924 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A716TY65
#2: Protein Cytolethal distending toxin subunit B family protein


Mass: 27191.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A718C6E5
#3: Protein Pertussis-like toxin subunit ArtA


Mass: 25117.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A716AET8

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Non-polymers , 5 types, 487 molecules

#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-ACN / ACETONE


Mass: 58.079 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H6O
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.12 Å3/Da / Density % sol: 60.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.4 / Details: 10% PEG10K, 0.1M sodium citrate and 15% acetone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.29→49.08 Å / Num. obs: 67108 / % possible obs: 99.73 % / Redundancy: 6.5 % / Biso Wilson estimate: 42.78 Å2 / CC1/2: 0.99 / Net I/σ(I): 16.61
Reflection shellResolution: 2.29→2.372 Å / Num. unique obs: 6544 / CC1/2: 0.719

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K6L

4k6l


Resolution: 2.29→49.08 Å / SU ML: 0.2576 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.6723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2088 3391 5.05 %
Rwork0.1702 63717 -
obs0.1721 67108 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.84 Å2
Refinement stepCycle: LAST / Resolution: 2.29→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8284 0 214 450 8948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00838656
X-RAY DIFFRACTIONf_angle_d1.016611681
X-RAY DIFFRACTIONf_chiral_restr0.06331259
X-RAY DIFFRACTIONf_plane_restr0.00551503
X-RAY DIFFRACTIONf_dihedral_angle_d20.27163080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.320.3281230.25392367X-RAY DIFFRACTION90.41
2.32-2.350.27561450.2322618X-RAY DIFFRACTION100
2.35-2.390.29741450.2242615X-RAY DIFFRACTION100
2.39-2.430.25111340.23042646X-RAY DIFFRACTION100
2.43-2.470.28821540.21552631X-RAY DIFFRACTION100
2.47-2.520.24771620.21342588X-RAY DIFFRACTION100
2.52-2.570.23141290.20462660X-RAY DIFFRACTION100
2.57-2.620.25061380.20092631X-RAY DIFFRACTION99.89
2.62-2.680.25011250.19252659X-RAY DIFFRACTION100
2.68-2.740.21011600.19382623X-RAY DIFFRACTION99.96
2.74-2.810.21261440.18972636X-RAY DIFFRACTION99.78
2.81-2.880.24441480.19072654X-RAY DIFFRACTION99.96
2.88-2.970.22731500.18762625X-RAY DIFFRACTION100
2.97-3.060.24581400.18372677X-RAY DIFFRACTION100
3.06-3.170.25161330.18042653X-RAY DIFFRACTION100
3.17-3.30.22021330.18072680X-RAY DIFFRACTION99.93
3.3-3.450.19941260.17432691X-RAY DIFFRACTION100
3.45-3.630.20061370.16392677X-RAY DIFFRACTION99.96
3.63-3.860.18011350.14792672X-RAY DIFFRACTION99.93
3.86-4.160.17641350.14532690X-RAY DIFFRACTION100
4.16-4.570.14581450.1272706X-RAY DIFFRACTION100
4.57-5.230.16821420.13092711X-RAY DIFFRACTION99.65
5.24-6.590.20181600.16782733X-RAY DIFFRACTION99.9
6.59-49.080.22581480.18092874X-RAY DIFFRACTION99.15

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