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- PDB-1n3g: Solution structure of the ribosome-associated cold shock response... -

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Basic information

Entry
Database: PDB / ID: 1n3g
TitleSolution structure of the ribosome-associated cold shock response protein Yfia of Escherichia coli
ComponentsProtein yfiA
KeywordsTRANSLATION / cold shock / translation inhibitor / dsRBD
Function / homology
Function and homology information


dormancy process / negative regulation of translational elongation / ribosomal small subunit binding / negative regulation of translational initiation / response to cold / cytosolic small ribosomal subunit / rRNA binding / cytosol
Similarity search - Function
Ribosome hibernation promotion factor-like / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosome-associated inhibitor A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / Torsion angle dynamics, simulated annealing
AuthorsRak, A. / Kalinin, A. / Shcherbakov, D. / Bayer, P.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2002
Title: Solution structure of the ribosome-associated cold shock response protein Yfia of Escherichia col
Authors: Rak, A. / Kalinin, A. / Shcherbakov, D. / Bayer, P.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: A protein residing at the subunit interface of the bacterial ribosome
Authors: Agafonov, D.E. / Kolb, V.A. / Nazimov, I.V. / Spirin, A.S.
#2: Journal: J.BIOMOL.NMR / Year: 2002
Title: 1H, 13C and 15N resonance assignments of the ribosome-associated cold shock response protein Yfia of Escherichia coli
Authors: Kalinin, A. / Rak, A. / Shcherbakov, D. / Bayer, P.
History
DepositionOct 28, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 29, 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: Protein yfiA


Theoretical massNumber of molelcules
Total (without water)12,8041
Polymers12,8041
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)29 / 50structures with acceptable covalent geometry, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein yfiA / cold-shock protein Yfia / ribosome associated inhibitor RaiA


Mass: 12803.583 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET11c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AD49

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNHA
2223D 15N-separated NOESY
1313D 13C-separated NOESY
4442D NOESY
NMR detailsText: Hydrogen bonds were extracted from a series of 15N-HSQC spectra recorded in D2O; Assignment was done using triple-resonance spectra

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM Yfia, U-15N-13C; 50mM phosphate buffer, 50mM LiCl90% H2O/10% D2O
20.5mM Yfia, U-15N; 50mM phosphate buffer, 50mM LiCl90% H2O/10% D2O
30.5mM Yfia, U-15N; 50mM phosphate buffer, 50mM LiCl100% D2O
40.8mM Yfia; 50mM phosphate buffer, 50mM LiCl90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM LiCl, 50mM KH2PO4 6.5 ambient 300 K
250mM LiCl, 50mM KH2PO4 6.5 ambient 300 K
350mM LiCl, 50mM KH2PO4 6.5 ambient 300 K
450mM LiCl, 50mM KH2PO4 6.5 ambient 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.2Bruker, Rheinstetten, Germanyprocessing
NDEE2.03SpinUp, Dortmund, Germanydata analysis
VNMR6.1BVarian, Darmstadt, Germanycollection
AURELIA2.3Bruker, Rheinstetten, Germanydata analysis
CNS1Axel Bruengerrefinement
RefinementMethod: Torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 29

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