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- PDB-2k29: Structure of the DBD domain of E. coli antitoxin RelB -

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Basic information

Entry
Database: PDB / ID: 2k29
TitleStructure of the DBD domain of E. coli antitoxin RelB
ComponentsAntitoxin RelB
KeywordsTRANSCRIPTION / RelB / Ribbon-Helix-Helix / antitoxin / Repressor / Stress response / Transcription regulation
Function / homology
Function and homology information


toxin sequestering activity / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / DNA-templated transcription / regulation of DNA-templated transcription
Similarity search - Function
RelB antitoxin/Antitoxin DinJ / RelB antitoxin / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailsRibbon-helix-helix family transcriptional repressor
AuthorsLi, G. / Zhang, Y. / Inouye, M. / Ikura, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural mechanism of transcriptional autorepression of the Escherichia coli RelB/RelE antitoxin/toxin module.
Authors: Li, G.Y. / Zhang, Y. / Inouye, M. / Ikura, M.
History
DepositionMar 28, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antitoxin RelB
B: Antitoxin RelB


Theoretical massNumber of molelcules
Total (without water)12,0042
Polymers12,0042
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Antitoxin RelB


Mass: 6001.910 Da / Num. of mol.: 2 / Fragment: DNA binding domain, UNP residues 4-53
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: relB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: Ribbon-helix-helix family transcriptional repressor
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D C(CO)NH
1513D H(CCO)NH
1613D HNCO
1722D 1H-13C HSQC
1823D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
NMR detailsText: The structure was determined using a combination of NOE and residual dipolar coupling data.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1.0 mM [U-100% 13C; U-100% 15N] RelBN, 20 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 1 uM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1.0 mM [U-100% 13C; U-100% 15N] RelBN, 20 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 1 uM sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMRelBN[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate1
100 mMsodium chloride1
1 mMDTT1
1 uMsodium azide1
0.5 mMRelBN[U-100% 13C; U-100% 15N]2
20 mMsodium phosphate2
100 mMsodium chloride2
1 mMDTT2
1 uMsodium azide2
Sample conditionsIonic strength: 0.12 / pH: 7.0 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
VNMR6.1CVariancollection
XEASYBartels et al.chemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2994 / NOE intraresidue total count: 708 / NOE long range total count: 712 / NOE medium range total count: 754 / NOE sequential total count: 820 / Hydrogen bond constraints total count: 104
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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