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- PDB-2an7: Solution structure of the bacterial antidote ParD -

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Basic information

Entry
Database: PDB / ID: 2an7
TitleSolution structure of the bacterial antidote ParD
ComponentsProtein parD
KeywordsDNA BINDING PROTEIN / bacterial antidote / ribbon-helix-helix / DNA-binding motif / plasmid addiction
Function / homology
Function and homology information


plasmid partitioning / toxin sequestering activity / protein heterotetramerization / sequence-specific DNA binding / negative regulation of DNA-templated transcription / protein homodimerization activity
Similarity search - Function
Antitoxin ParD / Antitoxin ParD / Arc Repressor Mutant / Antitoxin ParD / Antitoxin ParD superfamily / Ribbon-helix-helix / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsOberer, M. / Zangger, K. / Gruber, K. / Keller, W.
Citation
Journal: Protein Sci. / Year: 2007
Title: The solution structure of ParD, the antidote of the ParDE toxin antitoxin module, provides the structural basis for DNA and toxin binding.
Authors: Oberer, M. / Zangger, K. / Gruber, K. / Keller, W.
#1: Journal: Biochem.J. / Year: 2002
Title: The anti-toxin ParD of plasmid RK2 consists of two structurally distinct moieties and belongs to the ribbon-helix-helix family of DNA-binding proteins
Authors: Oberer, M. / Zangger, K. / Prytulla, S. / Keller, W.
History
DepositionAug 11, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
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 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein parD
B: Protein parD


Theoretical massNumber of molelcules
Total (without water)18,2292
Polymers18,2292
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 150structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Protein parD


Mass: 9114.252 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: RK2-RP4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P22995

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
13313C,15N-edited, 13C,15N-filtered NOESY-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6mM ParD U-15N,13C; 20mM phosphate buffer pH 6.0; 50mM KCL, 0.1% NaN3, 90% H2O, 10% D2O90% H2O/10% D2O
20.6mM ParD U-15N; 20mM phosphate buffer pH 6.0; 50mM KCL, 0.1% NaN3, 90% H2O, 10% D2O90% H2O/10% D2O
30.3mM ParD U-15N, 13C + 0.3mM ParD unlabeled; 20mM phosphate buffer pH 6.0; 50mM KCL, 0.1% NaN3, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 180mM / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1refinement
CNS1.1A.Brunger et al.structure solution
NMRPipe2005F.Delaglioprocessing
NMRView4.6B.Johnsondata analysis
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: 150 / Conformers submitted total number: 24

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