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- PDB-2kc8: Structure of E. coli toxin RelE (R81A/R83A) mutant in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2kc8
TitleStructure of E. coli toxin RelE (R81A/R83A) mutant in complex with antitoxin RelBc (K47-L79) peptide
Components
  • Antitoxin RelB
  • Toxin relE
KeywordsToxin/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 / endonuclease activity / Hydrolases; Acting on ester bonds / transcription cis-regulatory region binding / negative regulation of translation / rRNA binding / response to antibiotic / DNA-templated transcription / regulation of DNA-templated transcription
Similarity search - Function
RelB antitoxin/Antitoxin DinJ / RelB antitoxin / ParE toxin of type II toxin-antitoxin system, parDE / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Arc-type ribbon-helix-helix / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
mRNA interferase toxin RelE / Antitoxin RelB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsLi, G. / Zhang, Y. / Inouye, M. / Ikura, M.
CitationJournal: 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
DepositionDec 17, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toxin relE
B: Antitoxin RelB


Theoretical massNumber of molelcules
Total (without water)15,4922
Polymers15,4922
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Toxin relE


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
#2: Protein/peptide Antitoxin RelB


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: There is a related deposition of toxin RelE in the peptide free state
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D C(CO)NH
1413D H(CCO)NH
1513D HNCO
1613D 1H-15N NOESY
1732D 1H-13C HSQC
1833D (H)CCH-COSY
1933D (H)CCH-TOCSY
11033D 1H-13C NOESY
11122D 1H-15N HSQC
11223D HN(CA)CB
11323D C(CO)NH
11423D H(CCO)NH
11523D HNCO
11623D 1H-15N NOESY
11742D 1H-13C HSQC
11843D (H)CCH-COSY
11943D (H)CCH-TOCSY
12043D 1H-13C NOESY
12133D X-filtered 1H-13C NOESY
12243D X-filtered 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-13C; U-15N] RelE-1, 0.5 mM RelBc-2, 25 mM sodium phosphate-3, 500 mM sodium chloride-4, 1 mM DTT-5, 0.5 mM sodium azide-6, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM RelE-7, 0.5 mM [U-13C; U-15N] RelBc-8, 25 mM sodium phosphate-9, 500 mM sodium chloride-10, 1 mM DTT-11, 0.5 mM sodium azide-12, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-13C; U-15N] RelE-13, 0.5 mM RelBc-14, 25 mM sodium phosphate-15, 500 mM sodium chloride-16, 1 mM DTT-17, 0.5 mM sodium azide-18, 100% D2O100% D2O
40.5 mM RelE-19, 0.5 mM [U-13C; U-15N] RelBc-20, 25 mM sodium phosphate-21, 500 mM sodium chloride-22, 1 mM DTT-23, 0.5 mM sodium azide-24, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMRelE-1[U-13C; U-15N]1
0.5 mMRelBc-21
25 mMsodium phosphate-31
500 mMsodium chloride-41
1 mMDTT-51
0.5 mMsodium azide-61
0.5 mMRelE-72
0.5 mMRelBc-8[U-13C; U-15N]2
25 mMsodium phosphate-92
500 mMsodium chloride-102
1 mMDTT-112
0.5 mMsodium azide-122
0.5 mMRelE-13[U-13C; U-15N]3
0.5 mMRelBc-143
25 mMsodium phosphate-153
500 mMsodium chloride-163
1 mMDTT-173
0.5 mMsodium azide-183
0.5 mMRelE-194
0.5 mMRelBc-20[U-13C; U-15N]4
25 mMsodium phosphate-214
500 mMsodium chloride-224
1 mMDTT-234
0.5 mMsodium azide-244
Sample conditionsIonic strength: 0.5 / pH: 6.5 / Pressure: ambient / Temperature: 296.5 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichautomated noe peak assignments
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
MOLMOLKoradi, Billeter and Wuthrichstructure analysis
ProcheckNMRLaskowski and MacArthurdata analysis
VNMRVariancollection
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE 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 representativeSelection criteria: lowest energy
NMR ensembleAverage 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 rmsDistance rms dev: 0.012 Å / Distance rms dev error: 0.001 Å

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