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- PDB-2n3s: NMR Assignments and structure of Translation initiation factor IF... -

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Basic information

Entry
Database: PDB / ID: 2n3s
TitleNMR Assignments and structure of Translation initiation factor IF-1 from Burkholderia thailandensis E264.
ComponentsTranslation initiation factor IF-1
KeywordsTRANSLATION / Translation initiation factor / Burkholderia thailandensis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


translation initiation factor activity / ribosome binding / rRNA binding / cytoplasm
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. / Ribosomal protein S1-like 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
Translation initiation factor IF-1
Similarity search - Component
Biological speciesBurkholderia thailandensis E264 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsBarnwal, R. / Varani, G. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: NMR Assignments and structure of Translation initiation factor IF-1 from Burkholderia thailandensis E264.
Authors: Barnwal, R. / Varani, G.
History
DepositionJun 9, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Derived calculations / Category: struct_conf / struct_conf_type
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Translation initiation factor IF-1


Theoretical massNumber of molelcules
Total (without water)8,2321
Polymers8,2321
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)10 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Translation initiation factor IF-1


Mass: 8231.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis E264 (bacteria)
Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: infA, BTH_I3047 / Plasmid: pET28-AVA / Production host: Escherichia coli (E. coli) / References: UniProt: Q2SU48

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY

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Sample preparation

DetailsContents: 1.2 mM [U-95% 13C; U-95% 15N] Translation initiation factor IF, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 1.2 mM / Component: Translation initiation factor IF-1-1 / Isotopic labeling: [U-95% 13C; U-95% 15N]
Sample conditionspH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CCPNMRCCPNchemical shift assignment
CCPNMRCCPNdata analysis
CCPNMRCCPNpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
TALOSCornilescu, Delaglio and Baxstructure solution
CYANAGuntert, Mumenthaler and Wuthrichgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 10

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