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- PDB-2ro3: RDC-refined Solution Structure of the N-terminal DNA Recognition ... -

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Basic information

Entry
Database: PDB / ID: 2ro3
TitleRDC-refined Solution Structure of the N-terminal DNA Recognition Domain of the Bacillus subtilis Transition-state Regulator Abh
ComponentsPutative transition state regulator abh
KeywordsTRANSCRIPTION / DNA-binding / Transcription regulation
Function / homology
Function and homology information


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
Putative transition state regulator Abh
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsResidual dipolar coupling refined structure of AbhN
AuthorsSullivan, D.M. / Bobay, B.G. / Douglas, K.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 1.2Apr 4, 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: Putative transition state regulator abh
B: Putative transition state regulator abh


Theoretical massNumber of molelcules
Total (without water)12,3332
Polymers12,3332
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)10 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative transition state regulator abh


Mass: 6166.457 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: abh / Production host: Escherichia coli (E. coli) / References: UniProt: P39758

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Residual dipolar coupling refined structure of AbhN
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N IPAP HSQC

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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: 5.5 / 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 2185 NOE-derived distance constraints, 70 hydrogen bonds, 96 dihedral angle retraints, and 48 residual dipolar couplings
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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