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- PDB-2nxu: Atomic structure of translation initiation factor aIF2 beta-subun... -

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Basic information

Entry
Database: PDB / ID: 2nxu
TitleAtomic structure of translation initiation factor aIF2 beta-subunit from Archaebacteria sulfolobus solfataricus: high resolution NMR in solution
ComponentsTranslation initiation factor 2 beta subunit
KeywordsTRANSLATION / translation initiation factor / archaea / AIF2beta
Function / homology
Function and homology information


translation initiation factor activity
Similarity search - Function
Alpha-Beta Plaits - #3150 / Translation initiation factor 2, beta subunit / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5 / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Translation initiation factor 2 subunit beta
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodSOLUTION NMR / the structures were obtained by torsion angle dynamic calculation, energy minimization.
AuthorsVasile, F. / Pechkova, E. / Stolboushkina, E. / Garber, M. / Nicolini, C.
CitationJournal: Proteins / Year: 2007
Title: Solution structure of the beta-subunit of the translation initiation factor aIF2 from archaebacteria Sulfolobus solfataricus.
Authors: Vasile, F. / Pechkova, E. / Nicolini, C.
History
DepositionNov 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Translation initiation factor 2 beta subunit


Theoretical massNumber of molelcules
Total (without water)16,8291
Polymers16,8291
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 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Translation initiation factor 2 beta subunit / eIF-2-beta / aIF2-beta


Mass: 16828.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: eif2b / Plasmid: pET-28b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q97W59

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
NMR detailsText: The TOCSY spectra were performed with a mixing time of 80 ms. NOESY spectra were acquired with mixing time of 200 and 300 ms. For all spectra watergate was used as scheme for solvent ...Text: The TOCSY spectra were performed with a mixing time of 80 ms. NOESY spectra were acquired with mixing time of 200 and 300 ms. For all spectra watergate was used as scheme for solvent suppression. For the first six residues no signals were observed.

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Sample preparation

DetailsContents: concentration 10 mg/ml, 20 mM NaCl, 10% D2O in H2O
Solvent system: 10% D2O in H2O
Sample conditionsIonic strength: 0.2 M / pH: 8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XEASY1.3.13P. Guntert and K. Wuthrich et aldata analysis
DYANA1.5P. Guntert and K. Wuthrich et alstructure solution
GROMACS3.3.1David van der Spoel et al.refinement
RefinementMethod: the structures were obtained by torsion angle dynamic calculation, energy minimization.
Software ordinal: 1
Details: The structure were obtained using 635 non redundant NOE-derived distance restraints and were minimised with 1000 steps of conjugated gradient and 1000 of steepest discent. For the first six ...Details: The structure were obtained using 635 non redundant NOE-derived distance restraints and were minimised with 1000 steps of conjugated gradient and 1000 of steepest discent. For the first six residues no signals were observed.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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