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- PDB-9mlg: Xenorhabdus nematophilus XptA2 State 2, 1181insYWK1183, D1182T mutant -

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Basic information

Entry
Database: PDB / ID: 9mlg
TitleXenorhabdus nematophilus XptA2 State 2, 1181insYWK1183, D1182T mutant
ComponentsXptA2 protein
KeywordsTOXIN / TcA / Pore Forming Toxin
Function / homology
Function and homology information


: / TcdA1, receptor binding domain / 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 ...: / TcdA1, receptor binding domain / 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
Biological speciesXenorhabdus nematophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsAller, S.G. / Martin, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01HL128203 United States
CitationJournal: To Be Published
Title: Xenorhabdus nematophilus XptA2 State 2, YWKT mutant
Authors: Aller, S.G. / Martin, C.L. / Hill, J.H. / Wright, B.D. / Fernandez, S.R. / Lapi, S.E. / Miller, A.L. / Yoon, K.J.
History
DepositionDec 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)1,423,8485
Polymers1,423,8485
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
XptA2 protein


Mass: 284769.688 Da / Num. of mol.: 5 / Mutation: 1181insYWK1183, D1182T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenorhabdus nematophila (bacteria) / Gene: xptA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93RN7
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: A subunit of the Xenorhabdus nematophilus ABC Toxin Complex
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Xenorhabdus nematophila (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 10 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62247 / Symmetry type: POINT

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