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- PDB-2klm: Solution Structure of L11 with SAXS and RDC -

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Basic information

Entry
Database: PDB / ID: 2klm
TitleSolution Structure of L11 with SAXS and RDC
Components50S ribosomal protein L11
KeywordsRIBOSOMAL PROTEIN / L11 / RDC / SAXS / Methylation / Ribonucleoprotein / RNA-binding / rRNA-binding
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation
Similarity search - Function
Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12
Similarity search - Domain/homology
Large ribosomal subunit protein uL11
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION SCATTERING / SOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWang, J. / Zuo, X. / Yu, P. / Schwieters, C.D. / Wang, Y.
Citation
Journal: J.Am.Chem.Soc. / Year: 2009
Title: Determination of multicomponent protein structures in solution using global orientation and shape restraints.
Authors: Wang, J. / Zuo, X. / Yu, P. / Byeon, I.J. / Jung, J. / Wang, X. / Dyba, M. / Seifert, S. / Schwieters, C.D. / Qin, J. / Gronenborn, A.M. / Wang, Y.X.
#1: Journal: J. Mol. Biol. / Year: 2007
Title: The Structure of Free L11 and Functional Dynamics of L11 in Free, L11-rRNA(58nt) Binary and L11-rRNA(58nt)-thiostrepton Ternary Complexes
Authors: Lee, D. / Walsh, J. / Yu, P. / Markus, M. / Choli-papadopoulou, T. / Schwieters, C. / Krueger, S. / Draper, D. / Wang, Y.
History
DepositionJul 6, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 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: 50S ribosomal protein L11


Theoretical massNumber of molelcules
Total (without water)15,5261
Polymers15,5261
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein 50S ribosomal protein L11


Mass: 15526.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: rplK, rpl11 / Production host: Escherichia coli (E. coli) / References: UniProt: P36238

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Experimental details

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Experiment

Experiment
Method
SOLUTION SCATTERING
SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-100% 15N] entry-1, 95% H2O/5% D2O95% H2O/5% D2O
20.2 mM entry-2, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMentry-1[U-100% 15N]1
0.2 mMentry-22
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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Data collection

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz
Soln scatterType: x-ray / Buffer name: 50 MM NACL 20 MM MES / Conc. range: 1.0-5.0 / Data analysis software list: GNOM
Data reduction software list: MARDETECTOR, HOME- WRITTEN PROGRAM
Detector specific: HOME-MADE / Detector type: CCD CAMERA / Mean guiner radius: 2.05 nm / Mean guiner radius esd: 0.03 nm / Num. of time frames: 20 / Protein length: 0.5 / Sample pH: 6.5 / Source beamline: 12-ID / Source class: Y / Source type: APS ARGONNE / Temperature: 298 K

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Processing

NMR softwareName: X-PLOR NIH / Developer: Schwieters, Kuszewski, Tjandra and Clore / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10
Soln scatter modelConformer selection criteria: STRUCTURES WITH THE LOWEST ENERGY
Num. of conformers calculated: 100 / Num. of conformers submitted: 10 / Representative conformer: 1 / Software list: GNOM

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