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- PDB-2mt3: Structure of -24 DNA binding domain of sigma 54 from E.coli -

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Basic information

Entry
Database: PDB / ID: 2mt3
TitleStructure of -24 DNA binding domain of sigma 54 from E.coli
ComponentsRNA polymerase sigma-54 factor
KeywordsTRANSCRIPTION / Transcription regulation
Function / homology
Function and homology information


arginine metabolic process / DNA-binding transcription activator activity / submerged biofilm formation / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / nitrate assimilation / nucleotidyltransferase activity / cell motility / protein-DNA complex ...arginine metabolic process / DNA-binding transcription activator activity / submerged biofilm formation / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / nitrate assimilation / nucleotidyltransferase activity / cell motility / protein-DNA complex / DNA-templated transcription initiation / DNA-directed 5'-3' RNA polymerase activity / transcription cis-regulatory region binding / DNA binding
Similarity search - Function
Sigma-54 factors family signature 1. / 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
Similarity search - Domain/homology
RNA polymerase sigma-54 factor / RNA polymerase sigma-54 factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / na
Model detailslowest energy, model 1
AuthorsWemmer, D. / Gao, Z. / Pelton, J.
CitationJournal: To be Published
Title: Structure of -24 DNA binding domain of sigma 54 from E.coli
Authors: Gao, Z. / Pelton, J. / Wemmer, D.
History
DepositionAug 12, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Structure summary
Revision 1.2Feb 15, 2017Group: Database references
Revision 1.3Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / 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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase sigma-54 factor


Theoretical massNumber of molelcules
Total (without water)9,1601
Polymers9,1601
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RNA polymerase sigma-54 factor


Mass: 9160.482 Da / Num. of mol.: 1 / Fragment: residues 414-477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: rpoN, BN17_31451, BU34_12270, CF57_03485, CF58_26305, CF59_26290, CF60_25835, CF61_04260, ECs4081, LF82_1964
Production host: Escherichia coli (E. coli) / References: UniProt: C3SS82, UniProt: P24255*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D C(CO)NH
1413D HNCA
1513D HN(CA)CB
1613D H(CCO)NH
1713D (H)CCH-TOCSY
1813D HNHA
1913D 1H-15N NOESY
11013D 1H-15N TOCSY
11113D 1H-13C NOESY aliphatic
11213D (H)CCH-COSY
11313D HCACO
11413D HNCO

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Sample preparation

DetailsContents: 20 mM sodium phosphate, 200 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMsodium phosphate-11
200 mMsodium chloride-21
1 mMDTT-31
Sample conditionsIonic strength: 0.2 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANArefinement
RefinementMethod: na / Software ordinal: 1
NMR constraintsNOE constraints total: 539 / NOE intraresidue total count: 202 / NOE long range total count: 33 / NOE medium range total count: 104 / NOE sequential total count: 200
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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