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Yorodumi- PDB-5i4q: Contact-dependent inhibition system from Escherichia coli NC101 -... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i4q | |||||||||
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Title | Contact-dependent inhibition system from Escherichia coli NC101 - ternary CdiA/CdiI/EF-Tu complex (domains 2 and 3) | |||||||||
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 macromolecule metabolic process / primary metabolic process / guanyl-nucleotide exchange factor complex / : / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / toxin activity / endonuclease activity / Hydrolases; Acting on ester bonds ...macromolecule metabolic process / primary metabolic process / guanyl-nucleotide exchange factor complex / : / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / toxin activity / endonuclease 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 / SAD / Resolution: 2.35 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 | 5i4q.cif.gz | 169.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i4q.ent.gz | 139.7 KB | Display | PDB format |
PDBx/mmJSON format | 5i4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/5i4q ftp://data.pdbj.org/pub/pdb/validation_reports/i4/5i4q | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Hexamer according to size exclusion chromatography |
-Components
-Contact-dependent inhibitor ... , 2 types, 2 molecules AB
#1: Protein | Mass: 10476.635 Da / Num. of mol.: 1 / 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 |
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#2: Protein | Mass: 14227.428 Da / Num. of mol.: 1 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 |
-Protein , 1 types, 1 molecules C
#3: Protein | Mass: 23917.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Trypsin treatment prior to crystallization cleaved EF-Tu after Lys177 or after Arg172, however subsequent digestion in situ cannot be excluded. The sample is a mixture of tufA and tufB gene ...Details: Trypsin treatment prior to crystallization cleaved EF-Tu after Lys177 or after Arg172, however subsequent digestion in situ cannot be excluded. The sample is a mixture of tufA and tufB gene products (GI 947838, 948482). Source: (natural) Escherichia coli (E. coli) / References: UniProt: J7R9V6, UniProt: P0CE47*PLUS |
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-Non-polymers , 3 types, 94 molecules
#4: Chemical | ChemComp-CL / |
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#5: Chemical | ChemComp-SO4 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M NaCl, 0.1 M Bis-Tris pH 6.5, 1.5 M ammonium sulfate, trypsin 40 ng/microL, cryo 28% sucrose |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2015 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→30 Å / Num. obs: 23688 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 37.2 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.953 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.35→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 12.941 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.195 / 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: 55.144 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→30 Å
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