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Yorodumi- PDB-2kc8: Structure of E. coli toxin RelE (R81A/R83A) mutant in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kc8 | ||||||
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Title | Structure of E. coli toxin RelE (R81A/R83A) mutant in complex with antitoxin RelBc (K47-L79) peptide | ||||||
Components |
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Keywords | Toxin/Toxin Repressor / protein-protein complex / toxin RelE / antitoxin RelB / Repressor / Stress response / Toxin / Transcription / Transcription regulation / Toxin-Toxin Repressor COMPLEX | ||||||
Function / homology | Function and homology information toxin sequestering activity / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / DNA-binding transcription repressor activity / mRNA catabolic process / RNA endonuclease activity / cellular response to amino acid starvation / protein-DNA complex / ribosome binding ...toxin sequestering activity / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / DNA-binding transcription repressor activity / mRNA catabolic process / RNA endonuclease activity / cellular response to amino acid starvation / protein-DNA complex / ribosome binding / Hydrolases; Acting on ester bonds / rRNA binding / negative regulation of translation / transcription cis-regulatory region binding / response to antibiotic / DNA-templated transcription / regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, simulated annealing | ||||||
Authors | Li, G. / Zhang, Y. / Inouye, M. / Ikura, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Inhibitory mechanism of Escherichia coli RelE-RelB toxin-antitoxin module involves a helix displacement near an mRNA interferase active site. Authors: Li, G.Y. / Zhang, Y. / Inouye, M. / Ikura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kc8.cif.gz | 832.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kc8.ent.gz | 700.3 KB | Display | PDB format |
PDBx/mmJSON format | 2kc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kc8_validation.pdf.gz | 355.4 KB | Display | wwPDB validaton report |
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Full document | 2kc8_full_validation.pdf.gz | 604.1 KB | Display | |
Data in XML | 2kc8_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 2kc8_validation.cif.gz | 66.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/2kc8 ftp://data.pdbj.org/pub/pdb/validation_reports/kc/2kc8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11356.294 Da / Num. of mol.: 1 / Mutation: R81A, R83A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 Description: RelE is expressed with his-tag fusion. The his-tag is removed by thrombin afterward Gene: relE, b1563, JW1555 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P0C077 |
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#2: Protein/peptide | Mass: 4135.697 Da / Num. of mol.: 1 / Fragment: UNP residues 47-79 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 Description: RelBc (K47-L79) is expressed with GST-tag fusion. The GST-tag is removed by thrombin afterward Gene: relB, b1564, JW1556 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P0C079 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: There is a related deposition of toxin RelE in the peptide free state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.5 / pH: 6.5 / Pressure: ambient / Temperature: 296.5 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 3341 / NOE intraresidue total count: 801 / NOE long range total count: 690 / NOE medium range total count: 720 / NOE sequential total count: 782 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 77 / Protein psi angle constraints total count: 77 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 1.402 ° Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 2.588 ° / Maximum upper distance constraint violation: 0.353 Å / Torsion angle constraint violation method: CNS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.012 Å / Distance rms dev error: 0.001 Å |