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- PDB-2o9l: AMBER refined NMR Structure of the Sigma-54 RpoN Domain Bound to ... -

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Basic information

Entry
Database: PDB / ID: 2o9l
TitleAMBER refined NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element
Components
  • 5'-D(*GP*AP*AP*AP*CP*GP*TP*GP*CP*CP*AP*AP*AP*A)-3'
  • 5'-D(*TP*TP*TP*TP*GP*GP*CP*AP*CP*GP*TP*TP*TP*C)-3'
  • RNA polymerase sigma factor RpoN
KeywordsRNA POLYMERASE SIGMA FACTOR RPON/DNA / AMBER / GENERALIZED BORN SOLVENT MODEL / PROTEIN-DNA COMPLEX / HELIX-TURN-HELIX / TRANSCRIPTION FACTOR / SIGMA-54 / RNA POLYMERASE / RNA POLYMERASE SIGMA FACTOR RPON-DNA COMPLEX
Function / homology
Function and homology information


DNA-binding transcription activator activity / sigma factor activity / DNA-directed RNA polymerase complex / nucleotidyltransferase activity / 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
DNA / DNA (> 10) / RNA polymerase sigma factor RpoN
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsDoucleff, M. / Pelton, J.G. / Lee, P.S. / Wemmer, D.E.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural basis of DNA recognition by the alternative sigma-factor, sigma54.
Authors: Doucleff, M. / Pelton, J.G. / Lee, P.S. / Nixon, B.T. / Wemmer, D.E.
History
DepositionDec 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 5'-D(*TP*TP*TP*TP*GP*GP*CP*AP*CP*GP*TP*TP*TP*C)-3'
C: 5'-D(*GP*AP*AP*AP*CP*GP*TP*GP*CP*CP*AP*AP*AP*A)-3'
A: RNA polymerase sigma factor RpoN


Theoretical massNumber of molelcules
Total (without water)16,0483
Polymers16,0483
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)19 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: DNA chain 5'-D(*TP*TP*TP*TP*GP*GP*CP*AP*CP*GP*TP*TP*TP*C)-3'


Mass: 4252.761 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND
#2: DNA chain 5'-D(*GP*AP*AP*AP*CP*GP*TP*GP*CP*CP*AP*AP*AP*A)-3'


Mass: 4306.846 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND
#3: Protein RNA polymerase sigma factor RpoN


Mass: 7488.800 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: PSKB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) with Rosetta.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 C13-seperated[F1], C12-filtered[F2] NOESY
2223D C13-seperated NOESY
3333D 15N-seperated NOESY
1412D C12-filtered[F1,F2] NOESY
1512D C12-filtered[F1] NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM deuterated-HEPES, pH 6.9; 1 mM EDTA; 100% D2O100% D2O
21 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA; 90% H2O; 10% D2O90% H2O/10% D2O
31 mM Sigma-54-DNA (U-15N) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA; 90% H2O; 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1250 mM NaCl 6.9ambient 318 K
2250 mM NaCl 6.9ambient 303 K
3250 mM NaCl 6.9ambient 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio et al. 1995processing
NMRView5.0.4Johnson and Blevins. 1994data analysis
CYANA2.1Guntert. 2004structure solution
X-PLOR2.14Schwieters et al. 2003refinement
Amber7Case et al. 2002refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The 20-structure ensemble refined with XPLOR-NIH (PDB ID: 2O8K) were then subjected to 20 ps of simulated annealing using the SANDER module of AMBER 7.0 with the 1994 force field (ff94) and ...Details: The 20-structure ensemble refined with XPLOR-NIH (PDB ID: 2O8K) were then subjected to 20 ps of simulated annealing using the SANDER module of AMBER 7.0 with the 1994 force field (ff94) and the generalized Born solvent model. First, 0.5 ps of energy minimization was performed. Then simulated annealing was run from 300K to 0K using NMR distant and dihedral restraints, as well as a distance dependent dielectric and a nonbonding cutoff of 15A.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 19

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