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- PDB-1yfb: The solution structure of the N-domain of the transcription facto... -

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Basic information

Entry
Database: PDB / ID: 1yfb
TitleThe solution structure of the N-domain of the transcription factor abrB
ComponentsTransition state regulatory protein abrB
KeywordsTRANSCRIPTION / NMR / HOMODIMER / BIOINFORMATICS / SWAPPED-HAIRPIN BARREL
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 / simulated annealing
Model type detailsminimized average
AuthorsTruffault, V. / Djuranovic, S. / Coles, M.
CitationJournal: Structure / Year: 2005
Title: AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels.
Authors: Coles, M. / Djuranovic, S. / Soding, J. / Frickey, T. / Koretke, K. / Truffault, V. / Martin, J. / Lupas, A.N.
History
DepositionDec 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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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)13,9722
Polymers13,9722
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)1 / 50minimized average structure
RepresentativeModel #1minimized average structure

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Components

#1: Protein Transition state regulatory protein abrB


Mass: 6986.237 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ABRB / Plasmid: pet30b / Production host: Escherichia coli (E. coli) / References: UniProt: P08874

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 15N-separated NOESY
1212D NOESY
132HNHA
14313C-filtered/edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM AbrB-N; 20mM phosphate buffer; 80mM KCl90% H2O/10% D2O
20.5mM AbrB-N U-15N; 20mM phosphate buffer; 80mM KCl90% H2O/10% D2O
30.25mM AbrB-N U-15N, 0.25mM AbrB-N U-13C; 20mM phosphate buffer; 80mM KCl90% H2O/10% D2O
Sample conditionsIonic strength: 80mM / pH: 5.8 / Pressure: AMBIENT / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX7502
Bruker DMXBrukerDMX9003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORNIH-2.9.7BRUNGER, A.T.structure solution
XwinNMR3.5Brukercollection
XwinNMR3.5Brukerprocessing
NMRView5.0.15Johnson, B.A.data analysis
X-PLORNIH-2.9.7BRUNGER, A.T.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: minimized average structure / Conformers calculated total number: 50 / Conformers submitted total number: 1

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