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- PDB-1ny4: Solution structure of the 30S ribosomal protein S28E from Pyrococ... -

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Basic information

Entry
Database: PDB / ID: 1ny4
TitleSolution structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. Northeast Structural Genomics Consortium target JR19.
Components30S ribosomal protein S28E
KeywordsRNA BINDING PROTEIN / JR19 / AUTOSTRUCTURE / Ribosomal protein / Northeast Structural Genomics Consortium / PSI / Protein Structure Initiative / NESG
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
Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / 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 speciesPyrococcus horikoshii (archaea)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAramini, J.M. / Cort, J.R. / Huang, Y.J. / Xiao, R. / Acton, T.B. / Ho, C.K. / Shih, L.-Y. / Kennedy, M.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Protein Sci. / Year: 2003
Title: Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii.
Authors: Aramini, J.M. / Huang, Y.J. / Cort, J.R. / Goldsmith-Fischman, S. / Xiao, R. / Shih, L.-Y. / Ho, C.K. / Liu, J. / Rost, B. / Honig, B. / Kennedy, M.A. / Acton, T.B. / Montelione, G.T.
History
DepositionFeb 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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)9,3871
Polymers9,3871
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 / 56target function
RepresentativeModel #1lowest target function

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Components

#1: Protein 30S ribosomal protein S28E


Mass: 9386.690 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: RPS28E / Plasmid details: JR19-21 / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21MGK / References: UniProt: P61030

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-NOESY, 3D 13C-NOESY (aliphatic and aromatic)
1224D 13C-separated NOESY
131HNHA
143high resolution 13C,1H-HSQC
151H/D exchange
161backbone TR experiments, and 3D TOCSYs
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN. Manual side chain assignments. AUTOMATIC NOESY ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN. Manual side chain assignments. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND RESTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE RESTRAINTS WERE DETERMINED USING HYPER AND TALOS. BACKBONE CONFORMATIONS FOR RESIDUES 1-3, 5-6, 18-20, 22-23, 34-35, 48-49, 57-71, ARE NOT WELL-DEFINED [S(PHI) + S(PSI) < 1.8] IN THIS SOLUTION NMR STRUCTURE.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 MM JR19 U-15N,13C 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3, pH 6.55% D2O/95% H2O
21.0 MM JR19 U-15N,13C 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3, pH 6.5D2O
31.0 MM JR19 U-15N, 5%-13C 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3, pH 6.55% D2O/95% H2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 293 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
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA7503
Varian INOVAVarianINOVA6004
Varian INOVAVarianINOVA5005
Varian UNITYVarianUNITY6006

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVariancollection
NMRPipe2.1Delaglioprocessing
Sparky3.106Goddarddata analysis
AutoAssign1.9Zimmerman, Moseley, Montelionedata analysis
AutoStructure1.1.2Huang, Montelionerefinement
HYPER3.2Tejero, Montelionestructure solution
DYANA1.5Guntertrefinement
PdbStat3.27Tejero, Montelionestructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 828 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE RESTRAINTS, 99 DIHEDRAL ANGLE RESTRAINTS, AND 28 HYDROGEN BOND RESTRAINTS. (13.5 CONSTRAINTS PER ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 828 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE RESTRAINTS, 99 DIHEDRAL ANGLE RESTRAINTS, AND 28 HYDROGEN BOND RESTRAINTS. (13.5 CONSTRAINTS PER RESIDUE; 5.2 LONG-RANGE RESTRAINTS PER RESIDUE). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (DYANA). THE UNSTRUCTURED 11 RESIDUE C-TERMINAL TAG (AAALEHHHHHH) WAS INCLUDED IN THE STRUCTURE CALCULATIONS BUT IS OMITTED FROM THIS DEPOSITION.
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 56 / Conformers submitted total number: 10

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