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- PDB-5or5: NMR structure of the complex formed by an engineered region 2 of ... -

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Basic information

Entry
Database: PDB / ID: 5or5
TitleNMR structure of the complex formed by an engineered region 2 of sigmaE in complex with GTAAAA
Components
  • DNA (5'-D(*GP*TP*AP*AP*AP*A)-3')
  • ECF RNA polymerase sigma-E factor,ECF RNA polymerase sigma factor SigW,ECF RNA polymerase sigma-E factor
KeywordsTRANSCRIPTION / promoter melting / -10 element recognition / ECF sigma factor
Function / homology
Function and homology information


sigma factor antagonist complex / response to osmotic stress / response to temperature stimulus / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / cytosolic DNA-directed RNA polymerase complex / DNA-templated transcription initiation / negative regulation of DNA-templated transcription ...sigma factor antagonist complex / response to osmotic stress / response to temperature stimulus / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / cytosolic DNA-directed RNA polymerase complex / DNA-templated transcription initiation / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / plasma membrane / cytoplasm
Similarity search - Function
RNA polymerase sigma-W, bacillaceae / RNA polymerase sigma-70 RpoE type / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A / RNA polymerase sigma-70 region 2 ...RNA polymerase sigma-W, bacillaceae / RNA polymerase sigma-70 RpoE type / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / ECF RNA polymerase sigma-E factor / ECF RNA polymerase sigma factor SigW
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Bacillus subtilis (bacteria)
synthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsCampagne, S. / Vorholt, J.A. / Allain, F.H.
Citation
Journal: Not published
Title: Engineered promoter selectivity of an ECF sigma factor
Authors: Campagne, S. / Vorholt, J.A. / Allain, F.H.
#1: Journal: Nat. Struct. Mol. Biol. / Year: 2014
Title: Structural basis for -10 promoter element melting by environmentally induced sigma factors.
Authors: Campagne, S. / Marsh, M.E. / Capitani, G. / Vorholt, J.A. / Allain, F.H.
History
DepositionAug 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / pdbx_seq_map_depositor_info
Item: _pdbx_nmr_software.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation / pdbx_seq_map_depositor_info
Item: _citation.journal_abbrev / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3May 15, 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

Downloads & links

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Assembly

Deposited unit
A: ECF RNA polymerase sigma-E factor,ECF RNA polymerase sigma factor SigW,ECF RNA polymerase sigma-E factor
B: DNA (5'-D(*GP*TP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)12,7522
Polymers12,7522
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1250 Å2
ΔGint-4 kcal/mol
Surface area7050 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)13 / 30structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein ECF RNA polymerase sigma-E factor,ECF RNA polymerase sigma factor SigW,ECF RNA polymerase sigma-E factor / RNA polymerase sigma-E factor / Sigma-24 / ECF sigma factor SigW / Alternative RNA polymerase sigma ...RNA polymerase sigma-E factor / Sigma-24 / ECF sigma factor SigW / Alternative RNA polymerase sigma factor SigW / RNA polymerase sigma-W factor / Sigma-W factor / RNA polymerase sigma-E factor / Sigma-24


Mass: 10990.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Bacillus subtilis (bacteria)
Strain: K12, 168 / Gene: rpoE, sigE, b2573, JW2557, sigW, ybbL, BSU01730 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AGB6, UniProt: Q45585
#2: DNA chain DNA (5'-D(*GP*TP*AP*AP*AP*A)-3')


Mass: 1761.288 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic23D HN(CA)CB
122isotropic23D CBCA(CO)NH
132isotropic23D HNCO
142isotropic22D 1H-15N HSQC
152isotropic22D 1H-13C HSQC aliphatic
1122isotropic22D 1H-13C HSQC aromatic
1112isotropic13D 1H-13C NOESY aliphatic
1102isotropic13D 1H-13C NOESY aromatic
192isotropic13D 1H-15N NOESY
182isotropic23D H(CCO)NH
172isotropic23D C(CO)NH
163isotropic22D 1H-1H NOESY f2f
1133isotropic22D 1H-1H NOESY f1ff2f

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution21 mM [U-99% 13C; U-99% 15N] Engineered region2 of sigmaE from E. coli in which the loop L3 was replaced by the loop L3 of Bacillus subtilis sigmaW, 1 mM DNA (5'-D(*GP*TP*AP*AP*AP*A)-3'), 10 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O13C15N_H2090% H2O/10% D2O
solution31 mM [U-99% 13C; U-99% 15N] Engineered region2 of sigmaE from E. coli in which the loop L3 was replaced by the loop L3 of Bacillus subtilis sigmaW, 1 mM DNA (5'-D(*GP*TP*AP*AP*AP*A)-3'), 10 mM sodium phosphate, 50 mM sodium chloride, 100% D2O13C_15N_D20100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMEngineered region2 of sigmaE from E. coli in which the loop L3 was replaced by the loop L3 of Bacillus subtilis sigmaW[U-99% 13C; U-99% 15N]2
1 mMDNA (5'-D(*GP*TP*AP*AP*AP*A)-3')natural abundance2
10 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
1 mMEngineered region2 of sigmaE from E. coli in which the loop L3 was replaced by the loop L3 of Bacillus subtilis sigmaW[U-99% 13C; U-99% 15N]3
1 mMDNA (5'-D(*GP*TP*AP*AP*AP*A)-3')natural abundance3
10 mMsodium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
Sample conditionsIonic strength: 60 mM / Label: conditions / pH: 6.5 Not defined / Pressure: atmospheric atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III9001
Bruker AVANCE IIIBrukerAVANCE III7002

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CANDIDHerrmann, Guntert and Wuthrichpeak picking
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 13

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