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- PDB-1ovy: Solution Structure of Ribosomal Protein L18 from Bacillus stearot... -

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Basic information

Entry
Database: PDB / ID: 1ovy
TitleSolution Structure of Ribosomal Protein L18 from Bacillus stearothermophilus
Components50S Ribosomal Protein L18
KeywordsRIBOSOME / Ribosomal Protein
Function / homology
Function and homology information


5S rRNA binding / cytosolic large ribosomal subunit / structural constituent of ribosome / translation
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 speciesGeobacillus stearothermophilus (bacteria)
MethodSOLUTION NMR / Aria was used to select, assign peak lists from NOESY experiments. CNS as modified for use with ARIA was used for structure calculation using torsion angle simulated annealing.
AuthorsTurner, C.F. / Moore, P.B.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The solution structure of ribosomal protein L18 from Bacillus stearothermophilus
Authors: Turner, C.F. / Moore, P.B.
History
DepositionMar 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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: 50S Ribosomal Protein L18


Theoretical massNumber of molelcules
Total (without water)13,5011
Polymers13,5011
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 / 150structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein 50S Ribosomal Protein L18


Mass: 13500.638 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: RPLR / Plasmid: pET13a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09415

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D NOESY
1213D 15N-separated NOESY
1323D 13C-separated NOESY
NMR detailsText: This structure was determined using triple resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM L18 U-15N; 20mM phosphate buffer; 200mM NaCl; 5mM MgCl290% H2O/10% D2O
21.5mM L18 U-15N,13C; 20mM phosphate buffer; 200mM NaCl; 5mM MgCl290% H2O/10% D2O
31mM L18; 20mM phosphate buffer; 200mM NaCl; 5mM MgCl290% H2O/10% D2O
Sample conditionsIonic strength: 12mM KH2PO4; 8mM NaH2PO4; 200mM NaCl, 5mM MgCl2
pH: 6 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix97Biosym/MSIprocessing
Sparky3.93Goddard, T.D. & Kneller, D.G.data analysis
CNS1Brunger, A.T. et al.structure solution
ARIA1.2Linge, J.P. & Nilges, M.structure solution
CNS1Brunger, A.T. et al.refinement
ARIA1.2Linge, J.P. & Nilges, M.refinement
RefinementMethod: Aria was used to select, assign peak lists from NOESY experiments. CNS as modified for use with ARIA was used for structure calculation using torsion angle simulated annealing.
Software ordinal: 1
Details: The structures are based on a total of 2272 restraints. 1188 are unambiguous distance constraints, 913 are ambiguous distance constraints, 128 are dihedral angle restraints, and 43 are hydrogen bond restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 10

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