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- PDB-1ily: Solution Structure of Ribosomal Protein L18 of Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 1ily
TitleSolution Structure of Ribosomal Protein L18 of Thermus thermophilus
ComponentsRIBOSOMAL PROTEIN L18
KeywordsRNA BINDING PROTEIN / mixed alpha/beta
Function / homology
Function and homology information


rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm
Similarity search - Function
Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L18, bacterial-type / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein uL18
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsWoestenenk, E.A. / Gongadze, G.M. / Shcherbakov, D.V. / Rak, A.V. / Garber, M.B. / Hard, T. / Berglund, H.
CitationJournal: Biochem.J. / Year: 2002
Title: The solution structure of ribosomal protein L18 from Thermus thermophilus reveals a conserved RNA-binding fold.
Authors: Woestenenk, E.A. / Gongadze, G.M. / Shcherbakov, D.V. / Rak, A.V. / Garber, M.B. / Hard, T. / Berglund, H.
History
DepositionMay 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBOSOMAL PROTEIN L18


Theoretical massNumber of molelcules
Total (without water)9,8701
Polymers9,8701
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)27 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein RIBOSOMAL PROTEIN L18 /


Mass: 9869.507 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: RL18 / Organelle: RIBOSOME / Plasmid: pET11c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P80320

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1212D NOESY
1323D 15N-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM L18 U-15N,13C; 50 mM phosphate buffer; 200 mM LiCl90% H2O/10% D2O
21.3 mM L18 U-15N; 50 mM phosphate buffer; 200 mM LiCl90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM KH2PO4, 200 mM LiCl / pH: 5.9 / Pressure: 1 atm / Temperature: 303 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
Bruker AVANCEBrukerAVANCE6001
Varian INOVAVarianINOVA8002
Bruker AVANCEBrukerAVANCE5003
Bruker AVANCEBrukerAVANCE7004

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBrukercollection
NMRPipeDelaglioprocessing
ANSIG3.3Kraulisdata analysis
ANSIGfor WindowsHelgstranddata analysis
CNS1Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: structures are based on 1925 NOE-derived distance restraints, 125 backbone dihedral angle restraints, 12 chi-1 angle restraints, 68 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: 50 / Conformers submitted total number: 27

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