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Yorodumi- PDB-8uxt: Acinetobacter baumannii Tse15 Rhs effector, toxin cleavage mutant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8uxt | |||||||||
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Title | Acinetobacter baumannii Tse15 Rhs effector, toxin cleavage mutant (D1369N, D1391N) | |||||||||
Components | Tse15 | |||||||||
Keywords | TOXIN / Rhs-effector / Rhs cargo effector / Type 6 secretion system effector / Acinetobacter baumannii toxin / YD-repeat protein / T6SS. | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Acinetobacter baumannii AB307-0294 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.77 Å | |||||||||
Authors | Hayes, B.K. / Venugopal, H. / McGowan, S. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8uxt.cif.gz | 527.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8uxt.ent.gz | 431.3 KB | Display | PDB format |
PDBx/mmJSON format | 8uxt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8uxt_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8uxt_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8uxt_validation.xml.gz | 51.8 KB | Display | |
Data in CIF | 8uxt_validation.cif.gz | 76.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/8uxt ftp://data.pdbj.org/pub/pdb/validation_reports/ux/8uxt | HTTPS FTP |
-Related structure data
Related structure data | 42775MC 8uy4C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Recombinant Tse15(D1369N, D1391N) protein / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.183 MDa / Experimental value: NO |
Source (natural) | Organism: Acinetobacter baumannii AB307-0294 (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21 (bacteria) |
Buffer solution | pH: 8 / Details: 50 mM Hepes pH 8.0; 300 mM NaCl |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: 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 holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 1.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1163105 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
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