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- PDB-2khi: NMR structure of the domain 4 of the E. coli ribosomal protein S1 -

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Basic information

Entry
Database: PDB / ID: 2khi
TitleNMR structure of the domain 4 of the E. coli ribosomal protein S1
Components30S ribosomal protein S1
KeywordsRIBOSOMAL PROTEIN / ribosomal protein S1 / Acetylation / Phosphoprotein / Ribonucleoprotein / RNA-binding
Function / homology
Function and homology information


RNA secondary structure unwinding / positive regulation of cytoplasmic translation / negative regulation of cytoplasmic translation / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / single-stranded RNA binding / structural constituent of ribosome / translation / mRNA binding ...RNA secondary structure unwinding / positive regulation of cytoplasmic translation / negative regulation of cytoplasmic translation / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / single-stranded RNA binding / structural constituent of ribosome / translation / mRNA binding / RNA binding / membrane / cytoplasm
Similarity search - Function
Ribosomal protein S1 / Ribosomal protein S1-like / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Small ribosomal subunit protein bS1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsSalah, P. / Bisaglia, M. / Aliprandi, P. / Uzan, M. / Sizun, C. / Bontems, F.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Probing the relationship between Gram-negative and Gram-positive S1 proteins by sequence analysis
Authors: Salah, P. / Bisaglia, M. / Aliprandi, P. / Uzan, M. / Sizun, C. / Bontems, F.
History
DepositionApr 7, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 29, 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: 30S ribosomal protein S1


Theoretical massNumber of molelcules
Total (without water)13,0111
Polymers13,0111
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)12 / 10012 structures for lowest energy
RepresentativeModel #1

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Components

#1: Protein 30S ribosomal protein S1 /


Mass: 13010.658 Da / Num. of mol.: 1 / Fragment: UNP residues 267-361
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsA, ssyF, b0911, JW0894 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AG67

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-NOESY-HSQC
12213Caliphatic-NOESY-HSQC
1332D-NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-0.7mM [U-100% 15N] Domain 4 of the E. coli ribosomal protein S1-1, 95% H2O, 5% D2O95% H2O/5% D2O
20.5-0.7mM [U-100% 13C; U-100% 15N] Domain 4 of the E. coli ribosomal protein S1-2, 95% H2O/5% D2O95% H2O/5% D2O
30.5-0.7mM [U-100% 15N] Domain 4 of the E. coli ribosomal protein S1-3, 100% D2O100% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMDomain 4 of the E. coli ribosomal protein S1-1[U-100% 15N]0.5-0.71
mMDomain 4 of the E. coli ribosomal protein S1-2[U-100% 13C; U-100% 15N]0.5-0.72
mMDomain 4 of the E. coli ribosomal protein S1-3[U-100% 15N]0.5-0.73
Sample conditionsIonic strength: 200 / pH: 6.8 / Pressure: ambient / Temperature: 303 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
INCAGilquin B.structure solution
INCAGilquin B.refinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: 12 structures for lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 12 / Representative conformer: 1

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