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- PDB-2jxt: Solution structure of 50S ribosomal protein LX from Methanobacter... -

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Basic information

Entry
Database: PDB / ID: 2jxt
TitleSolution structure of 50S ribosomal protein LX from Methanobacterium thermoautotrophicum. Northeast Structural Genomics Consortium (NESG) target TR80
Components50S ribosomal protein LXRibosome
KeywordsRIBOSOMAL PROTEIN / 50S ribosomal protein LX / GFT NMR / NESG / Ribonucleoprotein / STRUCTURAL PROTEIN / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex
Similarity search - Function
Ubiquitin-like (UB roll) - #10 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein eL20
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodSOLUTION NMR / molecular dynamics, simulated annealing, distance geometry, torsion angle dynamics
AuthorsLiu, G. / Wang, D. / Nwosu, C. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. ...Liu, G. / Wang, D. / Nwosu, C. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution structure of 50S ribosomal protein LX from Methanobacterium thermoautotrophicum.
Authors: Liu, G. / Xiao, R. / Montelione, G.T.
History
DepositionNov 29, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 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 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / 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 LX


Theoretical massNumber of molelcules
Total (without water)10,3691
Polymers10,3691
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 #1lowest energy

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Components

#1: Protein 50S ribosomal protein LX / Ribosome


Mass: 10369.054 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H / Gene: rplX, MTH_1610 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / References: UniProt: O27647

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D SIMULTANEOUS CN-NOESY
1212D 1H-15N HSQC
1313D HNCO
1414,3D GFT CABCACONHN
1514,3D GFT HNNCABCA
1614,3D GFT (H)CCH
1714,3D GFT HABCAB(CO)NHN
1822D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.07 mM [U-100% 13C; U-100% 15N] 50S protein, 90% H2O/10% D2O90% H2O/10% D2O
21.1 mM [U-10% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.07 mMprotein[U-100% 13C; U-100% 15N]1
1.1 mMprotein[U-10% 13C; U-100% 15N]2
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichdata analysis
AutoStructure2.0.0Huang, Tejero, Powers and Montelionedata analysis
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMRVariancollection
RefinementMethod: molecular dynamics, simulated annealing, distance geometry, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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