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- PDB-1ne3: Solution structure of ribosomal protein S28E from Methanobacteriu... -

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Basic information

Entry
Database: PDB / ID: 1ne3
TitleSolution structure of ribosomal protein S28E from Methanobacterium Thermoautotrophicum. Ontario Centre for Structural Proteomics target MTH0256_1_68; Northeast Structural Genomics Target TT744
Components30S ribosomal protein S28E
KeywordsRIBOSOME / Beta protein / structural genomics / OCSP / NESG / PROTEIN STRUCTURE INITIATIVE / PSI / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


maturation of SSU-rRNA / ribosomal small subunit assembly / cytosolic small ribosomal subunit / structural constituent of ribosome / translation
Similarity search - Function
Nucleic acid-binding proteins / Ribosomal protein S28e / Ribosomal protein S28e / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Small ribosomal subunit protein eS28
Similarity search - Component
Biological speciesMethanothermococcus thermolithotrophicus (archaea)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsWu, B. / Pineda-Lucena, A. / Yee, A. / Cort, J.R. / Ramelot, T.A. / Kennedy, M. / Edwards, A. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Protein Sci. / Year: 2003
Title: Solution structure of ribosomal protein S28E from Methanobacterium thermoautotrophicum.
Authors: Wu, B. / Yee, A. / Pineda-Lucena, A. / Semesi, A. / Ramelot, T.A. / Cort, J.R. / Jung, J.W. / Edwards, A. / Lee, W. / Kennedy, M. / Arrowsmith, C.H.
History
DepositionDec 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 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: Database references / Derived calculations
Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_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: 30S ribosomal protein S28E


Theoretical massNumber of molelcules
Total (without water)7,6791
Polymers7,6791
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 / 100structures with the lowest energy,target function
RepresentativeModel #1lowest energy

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Components

#1: Protein 30S ribosomal protein S28E


Mass: 7679.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermococcus thermolithotrophicus (archaea)
Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O26356

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1mM mth0256, U-15N,13C; 450 mM Nacl, 25 mM Na2PO4, 1mM Benzamidine, 1x inhibitor cooktail, 0.01% NaN3, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 450 mM NaCl, 25 mM Phosphate buffer / pH: 6.5 / Pressure: ambient / Temperature: 298 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 INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.0.5Gunter, P.structure solution
CYANA1.0.5Gunter, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: 1055 NOE-derived distance constraints, 132 angle constraints (PHI, PSI and CHI)
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy,target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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