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- PDB-2n8n: Solution structure of translation initiation factor -

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Basic information

Entry
Database: PDB / ID: 2n8n
TitleSolution structure of translation initiation factor
ComponentsTranslation initiation factor IF-1
KeywordsTRANSLATION / translation initiation / RNA-binding
Function / homology
Function and homology information


translation initiation factor activity / ribosome binding / rRNA binding / cytoplasm / cytosol
Similarity search - Function
Translation initiation factor IF-1 / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / RNA-binding domain, S1 / Ribosomal protein S1-like RNA-binding domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Translation initiation factor IF-1 / Translation initiation factor IF-1
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsKim, D. / Lee, K. / Lee, B.
CitationJournal: Biochim.Biophys.Acta / Year: 2017
Title: Structure and dynamics study of translation initiation factor 1 from Staphylococcus aureus suggests its RNA binding mode
Authors: Kim, D.H. / Kang, S.J. / Lee, K.Y. / Jang, S.B. / Kang, S.M. / Lee, B.J.
History
DepositionOct 21, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _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

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Assembly

Deposited unit
A: Translation initiation factor IF-1


Theoretical massNumber of molelcules
Total (without water)8,2921
Polymers8,2921
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Translation initiation factor IF-1


Mass: 8291.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: Mu50 / Gene: infA, SAV2228 / Production host: Escherichia coli (E. coli) / References: UniProt: P65118, UniProt: Q2FW28*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HCACO
1313D HNCA
1413D HN(CO)CA
1513D HN(CA)CB
1613D HN(COCA)CB
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D (H)CCH-TOCSY
11013D 1H-15N TOCSY

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Sample preparation

DetailsContents: 0.1mM PMSF-1, 1mM EDTA-2, 50mM sodium chloride-3, 20mM MES-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.1 mMPMSF-11
1 mMEDTA-21
50 mMsodium chloride-31
20 mMMES-41
Sample conditionsIonic strength: 50 / pH: 6 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 730 / NOE intraresidue total count: 117 / NOE long range total count: 284 / NOE medium range total count: 78 / NOE sequential total count: 251
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.43 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.02 Å

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