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- PDB-6fi7: E.coli Sigma factor S (RpoS) Region 4 -

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Basic information

Entry
Database: PDB / ID: 6fi7
TitleE.coli Sigma factor S (RpoS) Region 4
ComponentsRNA polymerase sigma factor RpoS
KeywordsRNA BINDING PROTEIN / Apo-RpoS region 4 / Free RpoS region4
Function / homology
Function and homology information


bacterial-type RNA polymerase core enzyme binding / sigma factor antagonist complex / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-templated transcription initiation / negative regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
RNA polymerase sigma factor RpoS / Sigma-70 factors family signature 1. / 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 factor RpoS / Sigma-70 factors family signature 1. / 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
Similarity search - Domain/homology
RNA polymerase sigma factor RpoS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsLiu, B. / Matthews, S.J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: T7 phage factor required for managing RpoS inEscherichia coli.
Authors: Tabib-Salazar, A. / Liu, B. / Barker, D. / Burchell, L. / Qimron, U. / Matthews, S.J. / Wigneshweraraj, S.
History
DepositionJan 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conf
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase sigma factor RpoS


Theoretical massNumber of molelcules
Total (without water)10,0411
Polymers10,0411
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5100 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA polymerase sigma factor RpoS / Sigma S / Sigma-38


Mass: 10041.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rpoS, appR, katF, nur, otsX, sigS, b2741, JW5437 / Production host: Escherichia coli (E. coli) / References: UniProt: P13445

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HNCO
141isotropic13D HN(CA)CB
151isotropic13D (H)CCH-TOCSY
161isotropic13D HN(CO)CA
171isotropic13D HBHA(CO)NH
181isotropic23D 1H-15N NOESY
191isotropic23D 1H-13C NOESY aliphatic
1101isotropic23D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-99% 13C; U-99% 15N] E.coli Sigma factor S region 4, 93% H2O/7% D2O
Label: 13C_15N_sample / Solvent system: 93% H2O/7% D2O
SampleConc.: 1 mM / Component: E.coli Sigma factor S region 4 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 350 mM / Ionic strength err: 0.2 / Label: Condition / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Advance HD IIIBrukerAdvance HD III6001
Bruker Advance HD IIIBrukerAdvance HD III8002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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