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- PDB-2c06: NMR-based model of the complex of the toxin Kid and a 5-nucleotid... -

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Basic information

Entry
Database: PDB / ID: 2c06
TitleNMR-based model of the complex of the toxin Kid and a 5-nucleotide substrate RNA fragment (AUACA)
Components
  • 5'-R(*AP*UP*AP*CP*AP)-3'
  • KID TOXIN PROTEIN
KeywordsTOXIN / DOCKING / DNA REPLICATION / MAZF / PLASMID MAINTENANCE / POST SEGREGATIONAL KILLING / PROTEIN-RNA COMPLEX / RIBONUCLEASE / RNA CLEAVAGE / RNASE / TOXIN-ANTITOXIN
Function / homology
Function and homology information


endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding
Similarity search - Function
SH3 type barrels. - #110 / mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
RNA / Endoribonuclease PemK
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodSOLUTION NMR / HADDOCK
AuthorsKamphuis, M.B. / Bonvin, A.M.J.J. / Monti, M.C. / Lemonnier, M. / Munoz-Gomez, A. / Van Den Heuvel, R.H.H. / Diaz-Orejas, R. / Boelens, R.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Model for RNA Binding and the Catalytic Site of the Rnase Kid of the Bacterial Pard Toxin-Antitoxin System.
Authors: Kamphuis, M.B. / Bonvin, A.M.J.J. / Monti, M.C. / Lemonnier, M. / Munoz-Gomez, A. / Van Den Heuvel, R.H.H. / Diaz-Orejas, R. / Boelens, R.
History
DepositionAug 25, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Data collection / Other
Category: pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr ..._pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 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 1.5Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KID TOXIN PROTEIN
B: KID TOXIN PROTEIN
C: 5'-R(*AP*UP*AP*CP*AP)-3'


Theoretical massNumber of molelcules
Total (without water)25,3463
Polymers25,3463
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200LOWEST 10 ENERGY STRUCTURES IN LOWEST ENERGY CLUSTER
RepresentativeModel #1

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Components

#1: Protein KID TOXIN PROTEIN / PROTEIN PEMK


Mass: 11895.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: R1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P13976
#2: RNA chain 5'-R(*AP*UP*AP*CP*AP)-3'


Mass: 1554.008 Da / Num. of mol.: 1 / Source method: obtained synthetically
Compound detailsRESPONSIBLE FOR THE STABLE MAINTENANCE OF THE PLASMID DURING CELL DIVISION
Sequence detailsTHE DATABASE REFERENCE SEQUENCE FOR PEMK PROTEIN (UNIPROT ACCESSION NUMBER P13976) IS THE CLOSEST ...THE DATABASE REFERENCE SEQUENCE FOR PEMK PROTEIN (UNIPROT ACCESSION NUMBER P13976) IS THE CLOSEST MATCH TO KID TOXIN PROTEIN. THEIR SEQUENCES ARE IDENTICAL, HOWEVER PEMK HAS A LONG LEADER SEQUENCE NOT PRESENT IN KID TOXIN PROTEIN.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 1H-15N HSQC
NMR detailsText: THE STRUCTURE OF THE COMPLEX WAS DETERMINED WITH HADDOCK USING 28 AMBIGUOUS INTERACTION RESTRAINTS DERIVED FROM NMR CHEMICAL SHIFT PERTURBATION DATA, MUTAGENESIS DATA AND KNOWN RNA CLEAVAGE ...Text: THE STRUCTURE OF THE COMPLEX WAS DETERMINED WITH HADDOCK USING 28 AMBIGUOUS INTERACTION RESTRAINTS DERIVED FROM NMR CHEMICAL SHIFT PERTURBATION DATA, MUTAGENESIS DATA AND KNOWN RNA CLEAVAGE MECHANISM, USING THE CRYSTAL STRUCTURE OF THE KID DIMER (PDB ENTRY 1M1F) AS STARTING POINT. THE CHEMICAL SHIFT PERTURBATION DATA WERE OBTAINED BY ANALYSIS OF 1H-15N HSQC SPECTRA RECORDED WITH INCREASING RNA CONCENTRATIONS.

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Sample preparation

DetailsContents: 95% D2O / 5% WATER
Sample conditionsIonic strength: 100 mM / pH: 5.8 / Pressure: 1.0 atm / Temperature: 303.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
NMRViewstructure solution
CNSstructure solution
HADDOCKstructure solution
RefinementMethod: HADDOCK / Software ordinal: 1
Details: STRUCTURE OF THE COMPLEX WAS CALCULATED WITH HADDOCK FOLLOWING STANDARD PROTOCOLS DOMINGUEZ, BOELENS AND BONVIN, JACS 2003, 125, 1731-1737
NMR ensembleConformer selection criteria: LOWEST 10 ENERGY STRUCTURES IN LOWEST ENERGY CLUSTER
Conformers calculated total number: 200 / Conformers submitted total number: 10

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