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- PDB-8uxt: Acinetobacter baumannii Tse15 Rhs effector, toxin cleavage mutant... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8uxt
TitleAcinetobacter baumannii Tse15 Rhs effector, toxin cleavage mutant (D1369N, D1391N)
ComponentsTse15
KeywordsTOXIN / Rhs-effector / Rhs cargo effector / Type 6 secretion system effector / Acinetobacter baumannii toxin / YD-repeat protein / T6SS.
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds / hydrolase activity
Similarity search - Function
RHS protein / RHS protein / RHS repeat / RHS Repeat / YD repeat / : / Rhs repeat-associated core
Similarity search - Domain/homology
Biological speciesAcinetobacter baumannii AB307-0294 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.77 Å
AuthorsHayes, B.K. / Venugopal, H. / McGowan, S.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1165036 Australia
National Health and Medical Research Council (NHMRC, Australia)1128981 Australia
CitationJournal: Nat Commun / Year: 2024
Title: Structure of a Rhs effector clade domain provides mechanistic insights into type VI secretion system toxin delivery
Authors: Hayes, B.K. / Harper, M. / Venugopal, H. / Lewis, J.M. / Wright, A. / Lee, H.-C. / Steele, J.R. / Steer, D.L. / Schittenhelm, R.B. / Boyce, J.D. / McGowan, S.
History
DepositionNov 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tse15


Theoretical massNumber of molelcules
Total (without water)181,5451
Polymers181,5451
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Tse15


Mass: 181545.062 Da / Num. of mol.: 1 / Mutation: D1369N,D1391N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii AB307-0294 (bacteria)
Gene: ABBFA_02439 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Rosetta 2 / References: UniProt: A0A5K6CSR3
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: Recombinant Tse15(D1369N, D1391N) protein / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.183 MDa / Experimental value: NO
Source (natural)Organism: Acinetobacter baumannii AB307-0294 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 8 / Details: 50 mM Hepes pH 8.0; 300 mM NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 1.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1163105 / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00211506
ELECTRON MICROSCOPYf_angle_d0.46315587
ELECTRON MICROSCOPYf_dihedral_angle_d4.081554
ELECTRON MICROSCOPYf_chiral_restr0.0391660
ELECTRON MICROSCOPYf_plane_restr0.0032053

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