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- PDB-2k1n: DNA bound structure of the N-terminal domain of AbrB -

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Basic information

Entry
Database: PDB / ID: 2k1n
TitleDNA bound structure of the N-terminal domain of AbrB
Components
  • (DNA (25-MER)) x 2
  • AbrB family transcriptional regulator
KeywordsTRANSCRIPTION/DNA / AbrB / abrB8 / DNA bound / Transition State Regulator / DNA binding protein / Activator / DNA-binding / Repressor / Sporulation / Transcription / Transcription regulation / TRANSCRIPTION-DNA COMPLEX
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 ...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
DNA / DNA (> 10) / Transcriptional regulator for transition stateprotein / Transition state regulatory protein AbrB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Synthetic Construct (others)
MethodSOLUTION NMR / simulated annealing
Model detailsN-terminal domain of the Transition State Regulator AbrB bound to a DNA target (abrB8)
AuthorsCavanagh, J. / Bobay, B.G. / Sullivan, D.M. / Thompson, R.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 10, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type
Revision 1.3Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: DNA (25-MER)
F: DNA (25-MER)
A: AbrB family transcriptional regulator
B: AbrB family transcriptional regulator
C: AbrB family transcriptional regulator
D: AbrB family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)40,7226
Polymers40,7226
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (25-MER)


Mass: 7696.008 Da / Num. of mol.: 1 / Mutation: A10G / Source method: obtained synthetically / Source: (synth.) Synthetic Construct (others)
#2: DNA chain DNA (25-MER)


Mass: 7655.984 Da / Num. of mol.: 1 / Mutation: A10G / Source method: obtained synthetically / Source: (synth.) Synthetic Construct (others)
#3: Protein
AbrB family transcriptional regulator / AbrB/MazE/SpoVT family DNA-binding domain-containing protein / Transcriptional regulator for ...AbrB/MazE/SpoVT family DNA-binding domain-containing protein / Transcriptional regulator for transition stateprotein / Transition state regulatory protein AbrB


Mass: 6342.559 Da / Num. of mol.: 4 / Fragment: sequence database residues 3-57
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Species: subtilis
Gene: B4122_4520, B4417_1778, DFO69_4335, FAL52_19720, SC09_Contig28orf00381
Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: A0A063X7Z2, UniProt: P08874*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: N-terminal domain of the Transition State Regulator AbrB bound to a DNA target (abrB8)
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 0.5 mM [U-99% 15N] AbrBN55, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: AbrBN55 / Isotopic labeling: [U-99% 15N]
Sample conditionsIonic strength: 10 / pH: 5.5 / Pressure: ambient / Temperature: 305 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
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
HADDOCK1.3Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvinrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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