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- PDB-2m6p: The actinobacterial transcription factor RbpA binds to the princi... -

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Basic information

Entry
Database: PDB / ID: 2m6p
TitleThe actinobacterial transcription factor RbpA binds to the principal sigma subunit of RNA polymerase
Componentsuncharacterized protein Mb2076
KeywordsTRANSCRIPTION / mv2050 / MTB / RNAP / Sigma factor
Function / homologyRNA polymerase-binding protein A / Rubrerythrin, domain 2 / Single Sheet / Mainly Beta / :
Function and homology information
Biological speciesMycobacterium bovis (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing
Model detailslowest energy, model1
AuthorsLiu, B. / Parsy, M. / Paget, M. / Matthews, S.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: The actinobacterial transcription factor RbpA binds to the principal sigma subunit of RNA polymerase.
Authors: Tabib-Salazar, A. / Liu, B. / Doughty, P. / Lewis, R.A. / Ghosh, S. / Parsy, M.L. / Simpson, P.J. / O'Dwyer, K. / Matthews, S.J. / Paget, M.S.
History
DepositionApr 6, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein Mb2076


Theoretical massNumber of molelcules
Total (without water)5,2141
Polymers5,2141
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: Protein/peptide uncharacterized protein Mb2076


Mass: 5213.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium bovis (bacteria) / Strain: ATCC BAA-935 / AF2122/97 / Gene: Mb2076 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7TZ33

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D C(CO)NH
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D (H)CCH-TOCSY
1913D HBHA(CO)NH
11013D 1H-15N NOESY
11113D 1H-13C NOESY

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Sample preparation

DetailsContents: 3 mM beta-mercaptoethanol, 500 mM sodium chloride, 20 mM TRIS, 100% D2O
Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
3 mMbeta-mercaptoethanol-11
500 mMsodium chloride-21
20 mMTRIS-31
Sample conditionsIonic strength: 0.5 / pH: 7.5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: distance geometry, 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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