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- PDB-2joy: NMR Structure of 50S Ribosomal Protein L14e from Sulfolobus Solfa... -

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Basic information

Entry
Database: PDB / ID: 2joy
TitleNMR Structure of 50S Ribosomal Protein L14e from Sulfolobus Solfataricus: Northeast Structural Genomics Consortium Target SSR105
Components50S ribosomal protein L14e
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / 50s ribosomal protein l14e / protein nmr / solution structure / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


ribosomal large subunit biogenesis / cytosolic large ribosomal subunit / structural constituent of ribosome / translation / RNA binding
Similarity search - Function
Ribosomal protein L14e / SH3 type barrels. - #30 / Ribosomal protein L14 / Ribosomal protein L14, KOW motif / SH3 type barrels. / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Roll / Mainly Beta
Similarity search - Domain/homology
Large ribosomal subunit protein eL14
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsSingarapu, K.K. / Wu, Y. / Yee, A. / Semesi, A. / Arrowsmith, C. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR Structure of 50S Ribosomal Protein L14e; Northeast Structural Genomics Consortium Target SSR105
Authors: Singarapu, K.K. / Wu, Y. / Yee, A. / Semesi, A. / Arrowsmith, C. / Szyperski, T.
History
DepositionApr 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.6May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 50S ribosomal protein L14e


Theoretical massNumber of molelcules
Total (without water)10,8821
Polymers10,8821
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein 50S ribosomal protein L14e


Mass: 10881.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: rpl14e / Production host: Escherichia coli (E. coli) / References: UniProt: Q980C1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D HBHA(CO)NH
1714,3 D GFT (H)CCH COFY
1813D (H)CCH-COSY
1913D Simultanious NOESY

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] entity, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity[U-100% 13C; U-100% 15N]1
0.5 mMentity[U-10% 13C; U-99% 15N]2
Sample conditionsIonic strength: 320 / pH: 7.0 / 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 INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
AutoAssignZimmerman, Moseley, Kulikowski, Montelionedata analysis
AutoStructureHuang, Swapna, Rajan, Ke, Xia, Shukla, Inouye and Montelionerefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: CNS waterbath refinement is performed to refine the structure
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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