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- PDB-2kv5: Solution structure of the par toxin Fst in DPC micelles -

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Basic information

Entry
Database: PDB / ID: 2kv5
TitleSolution structure of the par toxin Fst in DPC micelles
ComponentsPutative uncharacterized protein RNAI
KeywordsTOXIN / toxin-antitoxin / bacterial
Function / homologyType I toxin-antitoxin system Fst family toxin
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsZangger, K. / Gobl, C. / Kosol, S. / Ruckert, H.M.
CitationJournal: Biochemistry / Year: 2010
Title: Solution structure and membrane binding of the toxin fst of the par addiction module
Authors: Gobl, C. / Kosol, S. / Stockner, T. / Ruckert, H.M. / Zangger, K.
History
DepositionMar 8, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein RNAI


Theoretical massNumber of molelcules
Total (without water)3,7671
Polymers3,7671
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)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Putative uncharacterized protein RNAI / Fst


Mass: 3767.479 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: synthesized by FMOC-based solid-phase peptide synthesis
Source: (synth.) Enterococcus faecalis (bacteria) / References: UniProt: Q9RLG7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 50mM potassium phosphate; 100mM [U-99% 2H] DPC; 0.02% sodium azide; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMpotassium phosphate-11
100 mMDPC-2[U-99% 2H]1
0.02 %sodium azide-31
Sample conditionsIonic strength: 0.15 / pH: 5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityVarianUNITY6001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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