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- PDB-2kjw: Solution structure and backbone dynamics of the permutant P54-55 -

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Basic information

Entry
Database: PDB / ID: 2kjw
TitleSolution structure and backbone dynamics of the permutant P54-55
Components30S ribosomal protein S6
KeywordsRIBOSOMAL PROTEIN / S6 permutant / solution structure / backbone dynamics / folding / Ribonucleoprotein / RNA-binding / rRNA-binding
Function / homology
Function and homology information


small ribosomal subunit rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / 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 1.2Nov 22, 2017Group: Database references / Derived calculations
Category: pdbx_database_related / pdbx_struct_assembly ...pdbx_database_related / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 30S ribosomal protein S6


Theoretical massNumber of molelcules
Total (without water)11,2591
Polymers11,2591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6840 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein 30S ribosomal protein S6 / TS9


Mass: 11258.886 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Permutant of the ribosomal protein S6 from Thermus thermophilus
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 permutant S6p3
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1232D 1H-13C HSQC
1333D CBCA(CO)NH
1433D C(CO)NH
1533D HNCO
1633D HNCA
1733D HN(CA)CB
1833D HN(CO)CA
1933D (H)CCH-TOCSY
11033D 1H-13C NOESY
11112D 1H-15N HSQC
11213D 1H-15N TOCSY
11313D 1H-15N NOESY
11413D HNHA
11522D DQF-COSY
11622D 1H-1H TOCSY
11722D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8-1.2 mM [U-15N] entity-1, 20 mM MES-2, 50 mM sodium chloride-3, 95% H2O/5% D2O95% H2O/5% D2O
20.8-1.2 mM entity-4, 50 mM sodium chloride-5, 100% D2O100% D2O
30.8-1.2 mM [U-13C; U-15N] entity-6, 20 mM MES-7, 50 mM sodium chloride-8, 95% H2O/5% D2O95% H2O/5% 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
mMentity-6[U-13C; U-15N]0.8-1.23
20 mMMES-73
50 mMsodium chloride-83
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
XwinNMRBruker 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: 770 / NOE intraresidue total count: 213 / NOE long range total count: 116 / NOE medium range total count: 138 / NOE sequential total count: 303 / Protein phi angle constraints total count: 88 / 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: 200 / Conformers submitted total number: 20

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