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- PDB-1ywx: Solution Structure of Methanococcus maripaludis Protein MMP0443: ... -

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Basic information

Entry
Database: PDB / ID: 1ywx
TitleSolution Structure of Methanococcus maripaludis Protein MMP0443: The Northeast Structural Genomics Consortium Target MrR16
Components30S ribosomal protein S24eRibosome
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / GFT NMR / MrR16 / NESGC / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


ribosome / structural constituent of ribosome / translation
Similarity search - Function
RRM (RNA recognition motif) domain / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S24e / Ribosomal protein S24e / 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
30S ribosomal protein S24e
Similarity search - Component
Biological speciesMethanococcus maripaludis (archaea)
MethodSOLUTION NMR / simulated annealing torsion angle dynamics
AuthorsYang, C.S. / Acton, T. / Shen, Y. / Ma, L. / Liu, G. / Xiao, R. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution Structure of Methanococcus maripaludis Protein MMP0443: The Northeast Structural Genomics Consortium Target MrR16
Authors: Yang, C.S. / Acton, T. / Shen, Y. / Ma, L. / Liu, G. / Xiao, R. / Montelione, G.T. / Szyperski, T.
History
DepositionFeb 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 2, 2022Group: Atomic model / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 30S ribosomal protein S24e


Theoretical massNumber of molelcules
Total (without water)11,4721
Polymers11,4721
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)20 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein 30S ribosomal protein S24e / Ribosome


Mass: 11472.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Gene: rps24e / Production host: Escherichia coli (E. coli) / References: UniProt: P61193

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111GFT (4,3)D HNNCABCA
121GFT (4,3)D CABCA(CO)NHN
131GFT (4,3)D HABCAB(CO)NHN
141GFT (4,3)D (H)CCH
151Simultaneous Heteronuclear Resolved [1H,1H]-NOESY

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Sample preparation

DetailsContents: U-15N,13C
Solvent system: 5% D2O, 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, pH6.5
Sample conditionsIonic strength: N.A. / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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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 INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
PROSA6Guentert, Pprocessing
XEASY1.3.1.3Bartels, Cdata analysis
DYANA1.5Guentert, Pstructure solution
DYANA1.5Guentert, Prefinement
RefinementMethod: simulated annealing torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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