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- PDB-1tty: Solution structure of sigma A region 4 from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 1tty
TitleSolution structure of sigma A region 4 from Thermotoga maritima
ComponentsRNA polymerase sigma factor rpoD
KeywordsTRANSCRIPTION / sigma factor / rna polymerase / helix-turn-helix
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / DNA binding / cytoplasm
Similarity search - Function
RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 ...RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA polymerase sigma factor SigA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodSOLUTION NMR / simulated annealing in torsion angle space
AuthorsLambert, L.J. / Wei, Y. / Schirf, V. / Demeler, B. / Werner, M.H.
CitationJournal: Embo J. / Year: 2004
Title: T4 AsiA blocks DNA recognition by remodeling sigma(70) region 4
Authors: Lambert, L.J. / Wei, Y. / Schirf, V. / Demeler, B. / Werner, M.H.
History
DepositionJun 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: 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_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 2024Group: 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
A: RNA polymerase sigma factor rpoD


Theoretical massNumber of molelcules
Total (without water)10,3841
Polymers10,3841
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)22 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein RNA polymerase sigma factor rpoD / Sigma-A


Mass: 10384.335 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: RPOD, SIGA, TM1451 / Plasmid: pET-30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-SI / References: UniProt: P77994

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA

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Sample preparation

DetailsContents: phosphate buffered saline, pH 7.0, 1 mM protein / Solvent system: 96% H2O, 4% D2O
Sample conditionsIonic strength: 150 mM NaCl / pH: 7 / Pressure: 1 atm / Temperature: 308 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 DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.9.3Clore and Schweitersstructure solution
NMRPipe2.2Delagliodata analysis
Xplor-NIH2.9.3Clore and Schweitersrefinement
RefinementMethod: simulated annealing in torsion angle space / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 22

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