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- PDB-2fkx: Ribosomal protein s15 from thermus thermophilus, nmr recalculated... -

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Basic information

Entry
Database: PDB / ID: 2fkx
TitleRibosomal protein s15 from thermus thermophilus, nmr recalculated structure
Components30S ribosomal protein S15
KeywordsSTRUCTURAL PROTEIN / RIBOSOMAL PROTEIN / RNA-BINDING PROTEIN / RRNA-BINDING PROTEIN
Function / homology
Function and homology information


cytosolic small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
S15/NS1, RNA-binding / Ribosomal protein S15, bacterial-type / Ribosomal protein S15 signature. / Helix Hairpins / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / S15/NS1, RNA-binding / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Small ribosomal subunit protein uS15
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / SIMULATED ANNEALING, TORSION ANGLE DYNAMICS
AuthorsMalliavin, T.E.
Citation
Journal: Biophys.J. / Year: 2007
Title: The Conformational Landscape of the Ribosomal Protein S15 and Its Influence on the Protein Interaction with 16S RNA.
Authors: Crety, T. / Malliavin, T.E.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Solution structure of the ribosomal rna binding protein s15 from thermus thermophilus
Authors: Berglund, H. / Rak, A. / Serganov, A. / Garber, M. / Hard, T.
History
DepositionJan 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Derived calculations
Category: citation_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation_author.name
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 950THIS ENTRY 2FKX REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN 1AB3.MR ORIGINAL DATA ...THIS ENTRY 2FKX REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN 1AB3.MR ORIGINAL DATA DETERMINED BY AUTHOR: H.BERGLUND, A.RAK, A.SERGANOV, M.GARBER, T.HARD

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 30S ribosomal protein S15


Theoretical massNumber of molelcules
Total (without water)10,4471
Polymers10,4471
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein 30S ribosomal protein S15


Mass: 10447.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: rpsO, rps15 / Plasmid: PET11C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P80378

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: AUTHOR USED THE MR DATA FROM ENTRY 1AB3.

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Sample preparation

Sample conditionspH: 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 spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.DeLano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warren.structure solution
ARIA1.2Jens Linge, Sean O'Donoghue, Michael Nilgesstructure solution
ARIA1.2Jens Linge, Sean O'Donoghue, Michael Nilgesrefinement
RefinementMethod: SIMULATED ANNEALING, TORSION ANGLE DYNAMICS / Software ordinal: 1
Details: SIMULATED ANNEALING IN TORSION ANGLE SPACE AND IN CARTESIAN COORDINATES.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 18

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