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- PDB-5lbj: Solution structure of the bacterial toxin LdrD in Tetrafluorethanol -

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Basic information

Entry
Database: PDB / ID: 5lbj
TitleSolution structure of the bacterial toxin LdrD in Tetrafluorethanol
ComponentsSmall toxic polypeptide LdrD
KeywordsTOXIN / Helix bacterial toxin TA type I
Function / homologyType I toxin-antitoxin system, toxin Ldr / Toxin Ldr, type I toxin-antitoxin system / membrane / plasma membrane / Toxic polypeptide / Small toxic polypeptide LdrD
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsMeyer, N.H.
CitationJournal: to be published
Title: Solution structure of the bacterial toxin LdrD in Tetrafluorethanol
Authors: Meyer, N.H.
History
DepositionJun 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 19, 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: Small toxic polypeptide LdrD


Theoretical massNumber of molelcules
Total (without water)3,9211
Polymers3,9211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3450 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Small toxic polypeptide LdrD / Toxic polypeptide / small


Mass: 3920.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: A0A024LAZ7, UniProt: Q6BF25*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D TOCSY
131isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution / Contents: 1 mM 1H LdrD, trifluoroethanol/water / Label: 1H / Solvent system: trifluoroethanol/water
SampleConc.: 1 mM / Component: LdrD / Isotopic labeling: 1H
Sample conditionsIonic strength: 0 Not defined / Label: condition_1 / pH: 7 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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