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- PDB-1l4s: Solution structure of ribosome associated factor Y -

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Basic information

Entry
Database: PDB / ID: 1l4s
TitleSolution structure of ribosome associated factor Y
ComponentsProtein yfiA
KeywordsTRANSLATION / Ribosome Binding Protein
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 / simulated annealing, torsion angle dynamics
AuthorsYe, K. / Serganov, A. / Hu, W. / Patel, D.J.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: Ribosome-associated factor Y adopts a fold resembling a double-stranded RNA binding domain scaffold.
Authors: Ye, K. / Serganov, A. / Hu, W. / Garber, M. / Patel, D.J.
History
DepositionMar 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: 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 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: Protein yfiA


Theoretical massNumber of molelcules
Total (without water)12,6721
Polymers12,6721
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)20 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein yfiA / Ribosome Associated Factor Y


Mass: 12672.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YFIA / Plasmid: pET29b / 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
1113D 15N-separated NOESY
1232D NOESY
1343D 13C-separated NOESY
141HNHA
254J-MODULATED-HSQC
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM pY, U-15N; 10mM sodium phosphate; 50 mM NACL;pH 5.7; 93% H2O, 7% D2O93% H2O/7% D2O
21.5 mM pY, U-15N,13C; 10mM sodium phosphate; 50 mM NACL;pH 5.7; 93% H2O, 7% D2O93% H2O/7% D2O
32 mM pY, U-15N; 10mM sodium phosphate; 50 mM NACL;pH 5.7; 100% D2O100% D2O
41.5 mM pY, U-15N,13C; 10mM sodium phosphate; 50 mM NACL;pH 5.7; 100% D2O100% D2O
51 mM pY, U-15N,13C; 20mM potassium phosphate;pH 6.6; 3.2% (w/v) bicelle (DMPC:DHPC:CTAB=30:10:2, molar ratio); 93% H2O, 7% D2O93% H2O/7% D2O
61 mM pY, U-10% 13C;10mM sodium phosphate; 50 mM NACL;pH 5.7; 100% D2O93% H2O/7% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM phosphate Na; 50 mM NACL 5.7ambient 304.5 K
220 mM potassium phosphate 6.6ambient 313 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 spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVarian Associates, Inc.collection
Felix98MSIprocessing
NMRView5Johnson, B.A, & Blevins, R.A.data analysis
CNS1Brunger, A.T. et al.refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: The structure are based on a total of 2207 restraints, 1507 unambiguous and 408 ambiguous NOE-derived distance constraints, 72 distance constraints from hydrogen bonds, 75 dihedral angle ...Details: The structure are based on a total of 2207 restraints, 1507 unambiguous and 408 ambiguous NOE-derived distance constraints, 72 distance constraints from hydrogen bonds, 75 dihedral angle constraints, 65 JHNHA coupling constraints, 80 dipolar coupling constraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 20

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