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- PDB-1p94: NMR Structure of ParG symmetric dimer -

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Basic information

Entry
Database: PDB / ID: 1p94
TitleNMR Structure of ParG symmetric dimer
Componentsplasmid partition protein ParG
KeywordsCELL CYCLE / ribbon-helix-helix / dimer / DNA binding
Function / homology
Function and homology information


DNA-binding transcription repressor activity / core promoter sequence-specific DNA binding / transcription repressor complex / protein-DNA complex / nucleic acid binding / negative regulation of DNA-templated transcription / identical protein binding
Similarity search - Function
DNA partition complex, ParG / ParG / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Plasmid partition protein ParG
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodSOLUTION NMR / ARIA protocol (Nilges, M. et al., (1997) J. Mol. Biol. 269, 408-422) was used to deal with ambiguous distance restraints, for some NOE assignments.
Model type detailsminimized average
AuthorsGolovanov, A.P. / Barilla, D. / Golovanova, M. / Hayes, F. / Lian, L.Y.
Citation
Journal: Mol.Microbiol. / Year: 2003
Title: ParG, a protein required for active partition of bacterial plasmids, has a dimeric ribbon-helix-helix structure.
Authors: Golovanov, A.P. / Barilla, D. / Golovanova, M. / Hayes, F. / Lian, L.Y.
#1: Journal: Mol.Microbiol. / Year: 2000
Title: The partition system of multidrug resistance plasmid TP228 includes a novel protein that epitomizes an evolutionarily distinct subgroup of the ParA superfamily
Authors: Hayes, F.
History
DepositionMay 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: plasmid partition protein ParG
B: plasmid partition protein ParG


Theoretical massNumber of molelcules
Total (without water)17,3002
Polymers17,3002
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)11 / 20structures with the lowest energy,target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein plasmid partition protein ParG


Mass: 8649.849 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: parG / Plasmid: pET-22-b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KJ82

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1233D 15N-separated NOESY
1322D NOESY
NMR detailsText: BEST REPRESENTATIVE CONFORMER (MODEL 1) IN THIS ENSEMBLE WAS OBTAINED BY ENERGY MINIMIZATION OF THE AVERAGE STRUCTURE, CALCULATED FOR MODELS 2-11

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM ParG U-15N,13C; 100 mM NaCl, 50 mM phosphate buffer, 1 mM DTT; 90% H2O, 10% D2O90% H2O/10% D2O
21 mM ParG U-15N; 100 mM NaCl, 50 mM phosphate buffer, 1 mM DTT; 100% D2O100% D2O
31 mM ParG U-15N; 100 mM NaCl, 50 mM phosphate buffer, 1 mM DTT; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 150 mM / pH: 5.5 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio et al.processing
NMRView5.01Johnson and Blevinsdata analysis
ARIA1.1Nilges et al.structure solution
CNS1Brunger et al.structure solution
CNS1Brunger et al.refinement
RefinementMethod: ARIA protocol (Nilges, M. et al., (1997) J. Mol. Biol. 269, 408-422) was used to deal with ambiguous distance restraints, for some NOE assignments.
Software ordinal: 1
Details: The ParG structure is based on 2230 ambiguous NOE restraints, 82 hydrogen bond restraints, and 144 CSI-based dihedral angle restraints. N-terminal region of ParG (1-32) is unstructured. The ...Details: The ParG structure is based on 2230 ambiguous NOE restraints, 82 hydrogen bond restraints, and 144 CSI-based dihedral angle restraints. N-terminal region of ParG (1-32) is unstructured. The C-terminal region (33-76) is structured.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy,target function
Conformers calculated total number: 20 / Conformers submitted total number: 11

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