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- PDB-8tv0: XptA2 wild type -

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Basic information

Entry
Database: PDB / ID: 8tv0
TitleXptA2 wild type
ComponentsXptA2
KeywordsTOXIN / TcA / Insecticide / Translocase
Function / homology
Function and homology information


ABC toxin, N-terminal domain / ABC toxin N-terminal region / TcA receptor binding domain / TcA receptor binding domain / Insecticidal toxin complex/plasmid virulence protein / Tc toxin complex TcA, C-terminal TcB-binding domain / Neuraminidase-like domain / Salmonella virulence plasmid 28.1kDa A protein / Tc toxin complex TcA C-terminal TcB-binding domain / Neuraminidase-like domain
Similarity search - Domain/homology
A component of insecticidal toxin complex (Tc)
Similarity search - Component
Biological speciesXenorhabdus nematophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsMartin, C.L. / Aller, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01HL128203 United States
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structures of the Insecticidal Toxin Complex Subunit XptA2 Highlight Roles for Flexible Domains.
Authors: Cole L Martin / David W Chester / Christopher D Radka / Lurong Pan / Zhengrong Yang / Rachel C Hart / Elad M Binshtein / Zhao Wang / Lisa Nagy / Lawrence J DeLucas / Stephen G Aller /
Abstract: The Toxin Complex (Tc) superfamily consists of toxin translocases that contribute to the targeting, delivery, and cytotoxicity of certain pathogenic Gram-negative bacteria. Membrane receptor ...The Toxin Complex (Tc) superfamily consists of toxin translocases that contribute to the targeting, delivery, and cytotoxicity of certain pathogenic Gram-negative bacteria. Membrane receptor targeting is driven by the A-subunit (TcA), which comprises IgG-like receptor binding domains (RBDs) at the surface. To better understand XptA2, an insect specific TcA secreted by the symbiont from the intestine of entomopathogenic nematodes, we determined structures by X-ray crystallography and cryo-EM. Contrary to a previous report, XptA2 is pentameric. RBD-B exhibits an indentation from crystal packing that indicates loose association with the shell and a hotspot for possible receptor binding or a trigger for conformational dynamics. A two-fragment XptA2 lacking an intact linker achieved the folded pre-pore state like wild type (wt), revealing no requirement of the linker for protein folding. The linker is disordered in all structures, and we propose it plays a role in dynamics downstream of the initial pre-pore state.
History
DepositionAug 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XptA2
B: XptA2
C: XptA2
D: XptA2
E: XptA2


Theoretical massNumber of molelcules
Total (without water)1,435,3225
Polymers1,435,3225
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.134, 176.934, 509.703
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
XptA2


Mass: 287064.375 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenorhabdus nematophila (bacteria) / Gene: xptA2 / Production host: Escherichia coli (E. coli) / References: UniProt: N1NRW3
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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 277 K / Method: liquid diffusion / Details: 0.1M HEPES, pH 7.5, 0.2M NaCl and 16-20% PEG-3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97932 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 3.1→48.8 Å / Num. obs: 271071 / % possible obs: 94.73 % / Redundancy: 3.3 % / CC1/2: 0.95 / Rmerge(I) obs: 0.09 / Net I/σ(I): 30.9
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.149 / Num. unique obs: 19970

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→48.73 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 3442 0.67 %
Rwork0.1939 --
obs0.1943 271034 91.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms100035 0 0 0 100035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002102065
X-RAY DIFFRACTIONf_angle_d0.525138570
X-RAY DIFFRACTIONf_dihedral_angle_d8.43713900
X-RAY DIFFRACTIONf_chiral_restr0.03915530
X-RAY DIFFRACTIONf_plane_restr0.00418005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.140.3102830.283412464X-RAY DIFFRACTION57
3.14-3.190.29561020.272713614X-RAY DIFFRACTION62
3.19-3.230.4123920.275314967X-RAY DIFFRACTION68
3.23-3.290.33211110.268116288X-RAY DIFFRACTION74
3.29-3.340.28971310.260517658X-RAY DIFFRACTION80
3.34-3.40.29171330.246519057X-RAY DIFFRACTION86
3.4-3.460.29681240.238520179X-RAY DIFFRACTION91
3.46-3.530.32631400.232221043X-RAY DIFFRACTION96
3.53-3.60.28491540.224221710X-RAY DIFFRACTION98
3.6-3.680.29111440.221221824X-RAY DIFFRACTION99
3.68-3.760.3111410.210121981X-RAY DIFFRACTION100
3.76-3.850.2371570.203221966X-RAY DIFFRACTION100
3.85-3.960.26281520.196522006X-RAY DIFFRACTION100
3.96-4.080.31191500.195122058X-RAY DIFFRACTION100
4.08-4.210.26361510.184622000X-RAY DIFFRACTION100
4.21-4.360.19291400.17522009X-RAY DIFFRACTION100
4.36-4.530.24471570.169422028X-RAY DIFFRACTION100
4.53-4.740.17721430.163121950X-RAY DIFFRACTION100
4.74-4.990.23841510.163622042X-RAY DIFFRACTION100
4.99-5.30.25391480.173422035X-RAY DIFFRACTION100
5.3-5.710.20821500.185722031X-RAY DIFFRACTION100
5.71-6.280.25571430.199622070X-RAY DIFFRACTION100
6.28-7.190.20671560.192122009X-RAY DIFFRACTION100
7.19-9.050.19821520.162821924X-RAY DIFFRACTION100
9.05-48.730.17181370.149719944X-RAY DIFFRACTION90

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