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- PDB-2h3a: Structural basis for nucleic acid and toxin recognition of the ba... -

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Basic information

Entry
Database: PDB / ID: 2h3a
TitleStructural basis for nucleic acid and toxin recognition of the bacterial antitoxin CcdA
Components
  • 5'-D(P*AP*TP*AP*TP*GP*TP*AP*TP*AP*CP*CP*CP*G)-3'
  • 5'-D(P*TP*CP*GP*GP*GP*TP*AP*TP*AP*CP*AP*TP*A)-3'
  • CcdA
KeywordsIMMUNE SYSTEM/DNA / ribbon-helix-helix / IMMUNE SYSTEM-DNA COMPLEX
Function / homology
Function and homology information


toxin sequestering activity / protein-containing complex disassembly / toxin-antitoxin complex / transcription repressor complex / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Arc Repressor Mutant - #80 / Post-segregation antitoxin CcdA / Post-segregation antitoxin CcdA / Arc Repressor Mutant / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Antitoxin CcdA / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsMadl, T. / Van Melderen, L. / Respondek, M. / Oberer, M. / Keller, W. / Zangger, K.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural Basis for Nucleic Acid and Toxin Recognition of the Bacterial Antitoxin CcdA
Authors: Madl, T. / Van Melderen, L. / Mine, N. / Respondek, M. / Oberer, M. / Keller, W. / Khatai, L. / Zangger, K.
History
DepositionMay 22, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(P*AP*TP*AP*TP*GP*TP*AP*TP*AP*CP*CP*CP*G)-3'
D: 5'-D(P*TP*CP*GP*GP*GP*TP*AP*TP*AP*CP*AP*TP*A)-3'
A: CcdA
B: CcdA


Theoretical massNumber of molelcules
Total (without water)24,7624
Polymers24,7624
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
Representative

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Components

#1: DNA chain 5'-D(P*AP*TP*AP*TP*GP*TP*AP*TP*AP*CP*CP*CP*G)-3'


Mass: 3950.598 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*TP*CP*GP*GP*GP*TP*AP*TP*AP*CP*AP*TP*A)-3'


Mass: 3990.622 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein CcdA / CcdA Conformer a


Mass: 8410.428 Da / Num. of mol.: 2 / Mutation: R70K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9S0Z5, UniProt: P62552*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM CcdA U-15N, 13C in complex with a 12 bp ccd OP DNA fragment; 20mM phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
20.5mM CcdA U-15N, 13C in complex with a 12 bp ccd OP DNA fragment; 20mM phosphate buffer, 100% D2O100% D2O
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brungerstructure solution
NMRPipeDelaglioprocessing
VNMRcollection
CNS1.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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