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- PDB-2ro4: RDC-refined Solution Structure of the N-terminal DNA Recognition ... -

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Basic information

Entry
Database: PDB / ID: 2ro4
TitleRDC-refined Solution Structure of the N-terminal DNA Recognition Domain of the Bacillus subtilis Transition-state Regulator AbrB
ComponentsTransition state regulatory protein abrB
KeywordsTRANSCRIPTION / Activator / DNA-binding / Repressor / Sporulation / Transcription regulation
Function / homology
Function and homology information


regulation of sporulation / sporulation resulting in formation of a cellular spore / negative regulation of DNA-templated transcription / DNA binding / identical protein binding
Similarity search - Function
AbrB, C-terminal / AbrB C-terminal domain / Pemi-like Protein 1; Chain: D / Pemi-like Protein 1; Chain: D - #10 / SpoVT / AbrB like domain / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SpoVT-AbrB domain superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Transition state regulatory protein AbrB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsRDC-refined structure of ABrBN
AuthorsSullivan, D.M. / Bobay, B.G. / Kojetin, D.J. / Thompson, R.J. / Rance, M. / Strauch, M.A. / Cavanagh, J.
CitationJournal: Structure / Year: 2008
Title: Insights into the nature of DNA binding of AbrB-like transcription factors
Authors: Sullivan, D.M. / Bobay, B.G. / Kojetin, D.J. / Thompson, R.J. / Rance, M. / Strauch, M.A. / Cavanagh, J.
History
DepositionMar 8, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 11, 2012Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transition state regulatory protein abrB
B: Transition state regulatory protein abrB


Theoretical massNumber of molelcules
Total (without water)12,2232
Polymers12,2232
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Transition state regulatory protein abrB


Mass: 6111.287 Da / Num. of mol.: 2 / Fragment: N-terminal DNA Recognition Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: abrB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08874

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: RDC-refined structure of ABrBN
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N IPAP HSQC
NMR detailsText: Experiments to measure residual dipolar couplings were collected and used to refine the previously released structure of AbrBN

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Sample preparation

DetailsContents: 20mM potassium phosphate, 15mM potassium chloride, 1mM EDTA, 1mM DTT, 0.02% sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMpotassium phosphate1
15 mMpotassium chloride1
1 mMEDTA1
1 mMDTT1
0.02 %sodium azide1
20 mMpotassium phosphate2
15 mMpotassium chloride2
1 mMEDTA2
1 mMDTT2
0.02 %sodium azide2
Sample conditionsIonic strength: 15 / pH: 5.8 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesdata analysis
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
NMRView5Johnson, One Moon Scientificdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
Details: The structures are based on 3090 NOE-derived distance constraints, 48 hydrogen bonds, 140 dihedral angle restraints, and 48 residual dipolar couplings restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10

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