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- PDB-2kjv: Solution structure and backbone dynamics of the ribosomal protein S6wt -

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Basic information

Entry
Database: PDB / ID: 2kjv
TitleSolution structure and backbone dynamics of the ribosomal protein S6wt
Components30S ribosomal protein S6
KeywordsRIBOSOMAL PROTEIN / S6 / solution structure / backbone dynamics / folding / Ribonucleoprotein / RNA-binding / rRNA-binding
Function / homology
Function and homology information


small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm
Similarity search - Function
Ribosomal protein S6/Translation elongation factor EF1B / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Translation elongation factor EF1B/ribosomal protein S6 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsOhman, A. / Oliveberg, M. / Oman, T.
Citation
Journal: Protein Sci. / Year: 2010
Title: Solution structures and backbone dynamics of the ribosomal protein S6 and its permutant P(54-55)
Authors: Ohman, A. / Oman, T. / Oliveberg, M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The HD-exchange motions of ribosomal protein S6 are insensitive to reversal of the protein-folding pathway
Authors: Haglund, E. / Lind, J. / Oman, T. / Ohman, A. / Maler, L. / Oliveberg, M.
History
DepositionJun 10, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 22, 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 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: 30S ribosomal protein S6


Theoretical massNumber of molelcules
Total (without water)11,9891
Polymers11,9891
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)20 / 300structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein 30S ribosomal protein S6 / TS9


Mass: 11988.753 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: rpsF, rps6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): pLysS / References: UniProt: P23370, UniProt: Q5SLP8*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure and backbone dynamics of the ribosomal protein S6wt
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N TOCSY
1313D 1H-15N NOESY
1413D HNHA
1522D DQF-COSY
1622D 1H-1H TOCSY
1722D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8-1.2 mM [U-15N] protein, 20 mM MES, 50 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
20.8-1.2 mM protein, 50 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-15N]0.8-1.21
20 mMMES-21
50 mMsodium chloride-31
mMentity-40.8-1.22
50 mMsodium chloride-52
Sample conditionspH: 6.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
xwinnmr/TOPSPINBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ANSIGKraulischemical shift assignment
ANSIGKraulisdata analysis
ANSIGKraulispeak picking
X-PLORBrungerstructure solution
X-PLORBrungergeometry optimization
X-PLORBrungerrefinement
AQUARullmann, Doreleijers and Kapteindata analysis
ProcheckNMRLaskowski and MacArthurstructure solution
TALOSCornilescu, Delaglio and Baxdata analysis
MOLMOLKoradi, Billeter and Wuthrichstructure solution
MULDERP. Padrta & V. Sklenardata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: sa.inp and refine.inp used with slight modifications.
NMR constraintsNOE constraints total: 745 / NOE intraresidue total count: 252 / NOE long range total count: 89 / NOE medium range total count: 97 / NOE sequential total count: 307 / Protein phi angle constraints total count: 90 / Protein psi angle constraints total count: 65
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 300 / Conformers submitted total number: 20

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