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- PDB-1n88: NMR structure of the ribosomal protein L23 from Thermus thermophilus. -

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Basic information

Entry
Database: PDB / ID: 1n88
TitleNMR structure of the ribosomal protein L23 from Thermus thermophilus.
ComponentsRibosomal protein L23
KeywordsTRANSLATION / NMR spectroscopy / protein structure / L23 / ribosome
Function / homology
Function and homology information


cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
RRM (RNA recognition motif) domain / Ribosomal protein L23 / Ribosomal protein L25/L23 / Ribosomal protein L23/L15e core domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein uL23
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, energy minimization
AuthorsOhman, A. / Rak, A. / Dontsova, M. / Garber, M.B. / Hard, T.
CitationJournal: J.Biomol.NMR / Year: 2003
Title: NMR structure of the ribosomal protein L23 from Thermus thermophilus.
Authors: Ohman, A. / Rak, A. / Dontsova, M. / Garber, M.B. / Hard, T.
History
DepositionNov 20, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 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_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
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: Ribosomal protein L23


Theoretical massNumber of molelcules
Total (without water)10,7601
Polymers10,7601
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 / 100accept.inp (XPLOR), low energy and good Ramachandran behaviour.
RepresentativeModel #1lowest energy

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Components

#1: Protein Ribosomal protein L23


Mass: 10759.808 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RA57

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
121CBCANH,CBCA(CO)NH,HNCO,HNCA,HN(CO)CA,C(CO)NH,HC(CO)NH,(H)CCH-COSY,(H)CCH-TOCSY
1323D 15N-separated NOESY
1422D 15N-HSQC,3D 15N-DIPSI-HSQC
1522D 1H-DQF-COSY, 2D 1H-clean-TOCSY, 2D 1H-NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM L23 U-15N,13C; 50mM KH2PO4, pH=5.1, 200mM LiCl290% H2O/10% D2O
20.8mM L23 U-15N; 50mM KH2PO4, pH=5.1, 200mM LiCl290% H2O/10% D2O
Sample conditionsIonic strength: 0.2M LiCl2 / pH: 5.1 / Pressure: 1 atm / Temperature: 308 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
Bruker AVANCEBrukerAVANCE5002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker Biospincollection
XwinNMR2.6Bruker Biospinprocessing
NMRPipe2.1Delaglio, F.processing
ANSIG1.02Helgstrand, M.data analysis
X-PLOR3.851refinement
AQUA3.2Laskowski, R.A.data analysis
TALOS1999.019.15.47Cornilescu, G.data analysis
MOLMOL2K.1Koradi, R.data analysis
RefinementMethod: simulated annealing, molecular dynamics, energy minimization
Software ordinal: 1
Details: Distance restraints: 1660 Dihedral angle restraints: 61
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: accept.inp (XPLOR), low energy and good Ramachandran behaviour.
Conformers calculated total number: 100 / Conformers submitted total number: 29

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