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- PDB-5ie8: The pyrazinoic acid binding domain of Ribosomal Protein S1 from M... -

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Basic information

Entry
Database: PDB / ID: 5ie8
TitleThe pyrazinoic acid binding domain of Ribosomal Protein S1 from Mycobacterium tuberculosis
Components30S ribosomal protein S1
KeywordsTRANSLATION / Tuberculosis / MtRpsA / Trans-translation / POA
Function / homology
Function and homology information


ribosome / RNA binding
Similarity search - Function
Ribosomal protein S1-like / RNA-binding domain, S1 / 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
30S ribosomal protein S1
Similarity search - Component
Biological speciesMycobacterium leprae (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsHuang, B. / Liao, X.
CitationJournal: Biomol NMR Assign / Year: 2016
Title: (1)H, (15)N, (13)C resonance assignments for pyrazinoic acid binding domain of ribosomal protein S1 from Mycobacterium tuberculosis
Authors: Huang, B. / Fu, J. / Guo, C. / Wu, X. / Lin, D. / Liao, X.
History
DepositionFeb 25, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 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 S1


Theoretical massNumber of molelcules
Total (without water)9,9921
Polymers9,9921
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5500 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)2 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein 30S ribosomal protein S1


Mass: 9992.364 Da / Num. of mol.: 1 / Fragment: UNP residues 280-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium leprae (strain TN) (bacteria)
Strain: TN / Gene: rpsA, ML1382 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: P46836

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-15N HSQC
121anisotropic13D HN(CA)CB
131anisotropic13D CBCA(CO)NH
141anisotropic13D HNCA
151anisotropic13D HNCO
171anisotropic13D HN(CO)CA
161anisotropic13D 1H-13C NOESY
1111anisotropic13D 1H-15N NOESY
1101anisotropic13D 1H-15N TOCSY
191anisotropic13D (H)CCH-TOCSY
181anisotropic13D CCH-TOCSY
1121anisotropic13D C(CO)NH
1131anisotropic13D HBHA(CO)NH
1141anisotropic13D H(CCO)NH

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Sample preparation

DetailsType: solution
Contents: 0.6 mM [U-99% 13C; U-99% 15N] MtRpsA, 90% H2O/10% D2O
Label: 15N 13C / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.6 mM / Component: MtRpsA / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 200 mM / Label: 15N 13C / pH: 6.3 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 850 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger A. T. et.al.refinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TopSpinBruker Biospin 3.2collection
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: 2

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