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- PDB-1z9b: Solution structure of the C1-subdomain of Bacillus stearothermoph... -

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Basic information

Entry
Database: PDB / ID: 1z9b
TitleSolution structure of the C1-subdomain of Bacillus stearothermophilus translation initiation factor IF2
ComponentsTranslation initiation factor IF-2
KeywordsTRANSLATION / protein synthesis translation intiation IF2 fMet-tRNA NMR structure
Function / homology
Function and homology information


translation initiation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Translation initiation factor IF- 2, domain 3 / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / : / Elongation factor G domain 2 ...Translation initiation factor IF- 2, domain 3 / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / : / Elongation factor G domain 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Translation initiation factor IF-2
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodSOLUTION NMR / intial fold determination with CNS in ARIA, iterative automatic assignment, simulated annealing in CYANA2.0, a round of annealing in ARIA, final water refinement using CNS procedure re_h2o.inp
AuthorsWienk, H. / Tomaselli, S. / Bernard, C. / Spurio, R. / Picone, D. / Gualerzi, C.O. / Boelens, R.
CitationJournal: Protein Sci. / Year: 2005
Title: Solution structure of the C1-subdomain of Bacillus stearothermophilus translation initiation factor IF2
Authors: Wienk, H. / Tomaselli, S. / Bernard, C. / Spurio, R. / Picone, D. / Gualerzi, C.O. / Boelens, R.
History
DepositionApr 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 22, 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: Translation initiation factor IF-2


Theoretical massNumber of molelcules
Total (without water)14,8161
Polymers14,8161
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Translation initiation factor IF-2


Mass: 14815.850 Da / Num. of mol.: 1 / Fragment: Bst IF2-C1 subdomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: infB / Plasmid: pEV / Production host: Escherichia coli (E. coli) / Strain (production host): JM109/pCI / Keywords: extra N-terminal 15 residue tail / References: UniProt: P04766

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY
1313D 13C-separated NOESY
141HNHA

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Sample preparation

DetailsContents: 0.5 mM Bst IF2-C1 U-15N & U-13C; 20 mM KPi; 200 mM KCl, protease inhibitor mix, NaN3
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 200 mM KCl / pH: 6.4 / Pressure: ambient / Temperature: 307.4 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker AVANCEBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5BRUKERcollection
NMRPipelinuxDelaglio et alprocessing
NMRView5.3Johnson and Blevinsdata analysis
CNS1.1Brunger et alrefinement
CYANA2Guentertstructure solution
TALOSdata analysis
RefinementMethod: intial fold determination with CNS in ARIA, iterative automatic assignment, simulated annealing in CYANA2.0, a round of annealing in ARIA, final water refinement using CNS procedure re_h2o.inp
Software ordinal: 1 / Details: TALOS and CSI used for dihedrals
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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