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Yorodumi- PDB-7rt7: Crystal structure of the RhsP2 C-terminal toxin domain in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rt7 | |||||||||
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Title | Crystal structure of the RhsP2 C-terminal toxin domain in complex with its immunity protein, RhsI2 | |||||||||
Components |
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Keywords | TOXIN/ANTITOXIN / Type Six Secretion System / Effector / Immunity / ADP-ribosyl transferase / RNA / Translation / Complex / TOXIN-ANTITOXIN complex | |||||||||
Function / homology | Function and homology information Domain of unknown function DUF6531 / Domain of unknown function (DUF6531) / RHS protein / RHS protein / RHS repeat / RHS Repeat / YD repeat / Rhs repeat-associated core Similarity search - Domain/homology | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.49 Å | |||||||||
Authors | Bullen, N.P. / Prehna, G. / Whitney, J.C. | |||||||||
Funding support | Canada, 2items
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Citation | Journal: Mol.Cell / Year: 2022 Title: An ADP-ribosyltransferase toxin kills bacterial cells by modifying structured non-coding RNAs. Authors: Bullen, N.P. / Sychantha, D. / Thang, S.S. / Culviner, P.H. / Rudzite, M. / Ahmad, S. / Shah, V.S. / Filloux, A. / Prehna, G. / Whitney, J.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rt7.cif.gz | 782.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rt7.ent.gz | 528.3 KB | Display | PDB format |
PDBx/mmJSON format | 7rt7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rt7_validation.pdf.gz | 535.9 KB | Display | wwPDB validaton report |
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Full document | 7rt7_full_validation.pdf.gz | 554 KB | Display | |
Data in XML | 7rt7_validation.xml.gz | 60.4 KB | Display | |
Data in CIF | 7rt7_validation.cif.gz | 81.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/7rt7 ftp://data.pdbj.org/pub/pdb/validation_reports/rt/7rt7 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 17019.033 Da / Num. of mol.: 6 / Fragment: C-terminal toxin domain (UNP residues 1473-1614) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria) Strain: UCBPP-PA14 / Gene: PA14_43100 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2Z8A2 #2: Protein | Mass: 16575.777 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria) Strain: UCBPP-PA14 Gene: DZ962_29645, IPC1164_23695, IPC737_11070, PA52Ts2_2703 Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A367GXM0 #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.94 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9.1 / Details: 1.05 M sodium citrate, 0.1 M CHES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→97.39 Å / Num. obs: 83716 / % possible obs: 99.85 % / Redundancy: 9.3 % / CC1/2: 0.994 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.5→2.55 Å / Num. unique obs: 4486 / CC1/2: 0.574 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.49→97.39 Å / Cross valid method: FREE R-VALUE / σ(F): 377.4 / Phase error: 22.7395 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.49→97.39 Å
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Refine LS restraints |
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LS refinement shell |
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