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- PDB-2mao: NMR structure of region 2 of E. coli sigmaE -

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Basic information

Entry
Database: PDB / ID: 2mao
TitleNMR structure of region 2 of E. coli sigmaE
ComponentsRNA polymerase sigma factor
KeywordsTRANSCRIPTION / ECF sigma factor
Function / homologyRNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsCampagne, S. / Vorholt, J.A. / Allain, F.H.-T.
CitationJournal: 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
DepositionJul 16, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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 / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase sigma factor


Theoretical massNumber of molelcules
Total (without water)12,2521
Polymers12,2521
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)18 / 30structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA polymerase sigma factor


Mass: 12251.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rpoE, EcDH1_1095, ECDH1ME8569_2500 / Production host: Escherichia coli (E. coli) / References: UniProt: C9R146

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: NMR structure of region 2 of E. coli sigmaE
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY aliphatic
11013D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: entity-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.07 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR softwareName: Amber / Version: 9
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo and Kollman
Classification: refinement
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: 18

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