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- PDB-1slj: Solution structure of the S1 domain of RNase E from E. coli -

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Basic information

Entry
Database: PDB / ID: 1slj
TitleSolution structure of the S1 domain of RNase E from E. coli
ComponentsRibonuclease E
KeywordsHYDROLASE / OB-fold / RNA-binding
Function / homology
Function and homology information


regulation of RNA helicase activity / rRNA 5'-end processing / ribonuclease E / ribonuclease E activity / bacterial degradosome / endoribonuclease complex / DEAD/H-box RNA helicase binding / 7S RNA binding / RNA catabolic process / tRNA processing ...regulation of RNA helicase activity / rRNA 5'-end processing / ribonuclease E / ribonuclease E activity / bacterial degradosome / endoribonuclease complex / DEAD/H-box RNA helicase binding / 7S RNA binding / RNA catabolic process / tRNA processing / mRNA catabolic process / RNA nuclease activity / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / protein complex oligomerization / protein homotetramerization / tRNA binding / molecular adaptor activity / rRNA binding / magnesium ion binding / RNA binding / zinc ion binding / identical protein binding / membrane / cytoplasm
Similarity search - Function
Polyribonucleotide phosphorylase C-terminal / Polyribonucleotide phosphorylase C terminal / : / RNase E/G, Thioredoxin-like domain / Ribonuclease E/G / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E / Ribonuclease E/G family / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain ...Polyribonucleotide phosphorylase C-terminal / Polyribonucleotide phosphorylase C terminal / : / RNase E/G, Thioredoxin-like domain / Ribonuclease E/G / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E / Ribonuclease E/G family / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsSchubert, M. / Edge, R.E. / Lario, P. / Cook, M.A. / Strynadka, N.C.J. / Mackie, G.A. / McIntosh, L.P.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces.
Authors: Schubert, M. / Edge, R.E. / Lario, P. / Cook, M.A. / Strynadka, N.C. / Mackie, G.A. / McIntosh, L.P.
History
DepositionMar 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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: Ribonuclease E


Theoretical massNumber of molelcules
Total (without water)10,7041
Polymers10,7041
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)10 / 200structures with the lowest energy
RepresentativeModel #4closest to the average

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Components

#1: Protein Ribonuclease E / RNase E


Mass: 10704.134 Da / Num. of mol.: 1 / Fragment: S1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RNE, AMS, HMP1, B1084 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P21513, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

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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
1313D 13C 15N/13C-separated NOESY
1413D 13C-separated NOESY aromatic
NMR detailsText: A mixing time of 100ms was used.

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Sample preparation

DetailsContents: 1.5mM RNase E S1 U-15N,13C; 20mM phosphate buffer; 50mM NaCl; 92% H2O, 8% D2O
Solvent system: 92% H2O, 8% D2O
Sample conditionsIonic strength: 75mM / pH: 6.5 / Pressure: ambient / Temperature: 303 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
Varian INOVAVarianINOVA6001
Varian UNITYVarianUNITY5002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglioprocessing
SparkyGoddarddata analysis
ARIA/CNSLingerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 2884 restraints, including 2113 unambiguous and 597 ambiguous NOE-derived distance constraints, 159 dihedral angle restraints, 15 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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