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- PDB-2ahq: Solution Structure of the C-terminal RpoN Domain of Sigma-54 from... -

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Basic information

Entry
Database: PDB / ID: 2ahq
TitleSolution Structure of the C-terminal RpoN Domain of Sigma-54 from Aquifex aeolicus
ComponentsRNA polymerase sigma factor RpoN
KeywordsTRANSCRIPTION / Sigma-54 / sigma factors / solution structure / RNA polymerase
Function / homology
Function and homology information


DNA-binding transcription activator activity / sigma factor activity / nucleotidyltransferase activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / DNA binding
Similarity search - Function
Sigma-54 factors family profile. / RNA polymerase sigma factor 54, core-binding domain / RNA polymerase sigma factor 54, DNA-binding / RNA polymerase sigma-54 factor, core-binding domain superfamily / Sigma-54 factor, Activator interacting domain (AID) / Sigma-54, DNA binding domain / Sigma-54 factor, core binding domain / Sigma-54 factors family signature 2. / RNA polymerase sigma factor 54 / Homeodomain-like ...Sigma-54 factors family profile. / RNA polymerase sigma factor 54, core-binding domain / RNA polymerase sigma factor 54, DNA-binding / RNA polymerase sigma-54 factor, core-binding domain superfamily / Sigma-54 factor, Activator interacting domain (AID) / Sigma-54, DNA binding domain / Sigma-54 factor, core binding domain / Sigma-54 factors family signature 2. / RNA polymerase sigma factor 54 / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA polymerase sigma factor RpoN
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDoucleff, M. / Malak, L.T. / Pelton, J.G. / Wemmer, D.E.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The C-terminal RpoN domain of sigma54 forms an unpredicted helix-turn-helix motif similar to domains of sigma70.
Authors: Doucleff, M. / Malak, L.T. / Pelton, J.G. / Wemmer, D.E.
History
DepositionJul 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
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: RNA polymerase sigma factor RpoN


Theoretical massNumber of molelcules
Total (without water)8,9661
Polymers8,9661
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)20 / 150target function
RepresentativeModel #1lowest dyana target function

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Components

#1: Protein RNA polymerase sigma factor RpoN / SIGMA-54


Mass: 8966.376 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: rpoN / Plasmid: pet21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (BL21 (DE3) with pLysS) / References: UniProt: O66858

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D N15-seperated TOCSY
132HNCA-J
142(H)CCH-TOCSY
1523D 13C-separated NOESY
1642D C13-HSQC
NMR detailsText: Other experiments performed and used for chemical shift assignments and obtaining restraints: CBCA(CO)NH, DQF-COSY, CC(CO)NH, H/D Exchange via N15-HSQC, HNHA - J couplings

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM Sigma-54 U-15N; 50 mM Hepes; 250 mM NaCl; 1 mM EDTA; 90% H20; 10% D2090% H20; 10% D20
20.8 mM Sigma-54 U-15N U-13C; 50 mM Hepes; 250 mM NaCl; 1 mM EDTA; 90% H20; 10% D2090% H20; 10% D20
30.8 mM Sigma-54 U-15; 50 mM Hepes; 250 mM NaCl; 1 mM EDTA; 5% H20; 95% D205% H20; 95% D20
40.8 mM Sigma-54 U-15N U-10% 13C; 50 mM Hepes; 250 mM NaCl; 1 mM EDTA; 90% H20; 10% D2090% H20; 10% D20
Sample conditionsIonic strength: 50 mM Hepes; 250 mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio et al. (1995)processing
NMRView5.0.4Johnson & Blevins (1994)data analysis
DYANA1.5Guntert et al. (1997)structure solution
DYANA1.5Guntert et al. (1997)refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Structures are based on a total 1064 restraints: 956 distance and 108 dihedral angle
NMR representativeSelection criteria: lowest dyana target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 150 / Conformers submitted total number: 20

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