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Yorodumi- PDB-5i4r: Contact-dependent inhibition system from Escherichia coli NC101 -... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i4r | |||||||||
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Title | Contact-dependent inhibition system from Escherichia coli NC101 - ternary CdiA/CdiI/EF-Tu complex (trypsin-modified) | |||||||||
Components |
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Keywords | TOXIN/ANTITOXIN / toxin / antitoxin / elongation factor / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes / UC4CDI / TOXIN-ANTITOXIN complex | |||||||||
Function / homology | Function and homology information primary metabolic process / macromolecule metabolic process / : / guanyl-nucleotide exchange factor complex / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / endonuclease activity / toxin activity / Hydrolases; Acting on ester bonds ...primary metabolic process / macromolecule metabolic process / : / guanyl-nucleotide exchange factor complex / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / endonuclease activity / toxin activity / Hydrolases; Acting on ester bonds / response to antibiotic / GTPase activity / GTP binding / RNA binding / extracellular region / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli NC101 (bacteria) Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||
Authors | Michalska, K. / Stols, L. / Eschenfeldt, W. / Hayes, C.S. / Goulding, C.W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI) | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs. Authors: Michalska, K. / Gucinski, G.C. / Garza-Sanchez, F. / Johnson, P.M. / Stols, L.M. / Eschenfeldt, W.H. / Babnigg, G. / Low, D.A. / Goulding, C.W. / Joachimiak, A. / Hayes, C.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i4r.cif.gz | 457.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i4r.ent.gz | 380.9 KB | Display | PDB format |
PDBx/mmJSON format | 5i4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5i4r_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5i4r_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5i4r_validation.xml.gz | 38.5 KB | Display | |
Data in CIF | 5i4r_validation.cif.gz | 53 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/5i4r ftp://data.pdbj.org/pub/pdb/validation_reports/i4/5i4r | HTTPS FTP |
-Related structure data
Related structure data | 5i4qSC 1ercS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 10476.635 Da / Num. of mol.: 2 / Fragment: toxin domain Source method: isolated from a genetically manipulated source Details: The cloned fragment corresponds to Val3035-Lys3289 of the full-length protein (CdiA-CT). The final purified ternary complex was treated with trypsin that cleaved CdiA-CT after Lys3196. Source: (gene. exp.) Escherichia coli NC101 (bacteria) / Strain: NC101 / Plasmid: pMCSG58 / Details (production host): dual expression vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Gold / References: UniProt: P0DSI1*PLUS #2: Protein/peptide | Mass: 4804.528 Da / Num. of mol.: 2 / Fragment: N-terminal / Source method: isolated from a natural source Details: Short trypsin treatment prior to crystallization cleaved EF-Tu after Arg45 and after Arg59. The sample is a mixture of tufA and tufB gene products (GI 947838, 948482). Source: (natural) Escherichia coli (E. coli) / Strain: BL21(DE3) / References: UniProt: A7ZSL4, UniProt: P0CE48*PLUS #3: Protein | Mass: 36966.277 Da / Num. of mol.: 2 / Fragment: C-terminal / Source method: isolated from a natural source Details: Short trypsin treatment prior to crystallization cleaved EF-Tu after Arg45 and after Arg59. The sample is a mixture of tufA and tufB gene products (GI 947838, 948482). Source: (natural) Escherichia coli (E. coli) / Strain: BL21(DE3) / References: UniProt: A7ZSL4, UniProt: P0CE47*PLUS #4: Protein | Mass: 14227.428 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli NC101 (bacteria) / Strain: NC101 / Plasmid: pMCSG58 / Details (production host): dual expression vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Gold / References: UniProt: P0DSM8*PLUS #5: Chemical | |
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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: 3.41 Å3/Da / Density % sol: 63.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.05 M KCl 0.1 M HEPES pH=7.0, 1.0 M ammonium sulfate, cryo 3.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2014 / Details: mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→30 Å / Num. obs: 26374 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 63.3 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 3.3→3.36 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 1.5 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5I4Q,1ERC Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.897 / SU B: 65.902 / SU ML: 0.431 / Cross valid method: THROUGHOUT / ESU R Free: 0.545 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 115.53 Å2
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Refinement step | Cycle: 1 / Resolution: 3.3→30 Å
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Refine LS restraints |
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