BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 7088

Title: dynamics within the fMet-tRNA binding domain of translation initiation factor IF2 from Bacillus stearothermophilus   PubMed: 16968770

Authors: Wienk, Hans; Tomaselli, Simona; Spurio, Roberto; Gualerzi, Claudio; Boelens, Rolf

Citation: Milon, P.; Tischenko, E.; Tomsic, J.; Caserta, E.; Folkers, G.; La Teana, A.; Rodnina, M.; Pon, C.; Boelens, Rolf; Gualerzi, Claudio. "The nucleotide-binding site of bacterial translation initiation factor 2 (IF2) as a metabolic sensor"  Proc. Natl. Acad. Sci. U.S.A. 103, 13962-13967 (2006).

Assembly members:
domain III-IV, polymer, 240 residues, 26759 Da.

Natural source:   Common Name: bacillus stearothermophilus   Taxonomy ID: 1422   Superkingdom: Eubacteria   Kingdom: not available   Genus/species: Bacillus stearothermophilus

Experimental source:   Production method: recombinant technology

Entity Sequences (FASTA):
domain III-IV: NEFELGTRGSSRVDLQEQRS VKTRVSLDDLFEQIKQGEMK ELNLIVKADVQGSVEALVAA LQKIDVEGVRVKIIHAAVGA ITESDISLATASNAIVIGFN VRPDANAKRAAESEKVDIRL HRIIYNVIEEIEAAMKGMLD EYEEKVIGQAEVRQTFKVSK VGTIAGCYVTDGKITRDSKV RLIRQGIVVYEGEIDSLKRY KDDVREVAQGYECGLTIKNF NDIKEGDVIEAYVMQEVARA

Data sets:
Data typeCount
13C chemical shifts332
15N chemical shifts163
1H chemical shifts163
heteronuclear NOE values143
T1 relaxation values145
T2 relaxation values145

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1IF2 domain III-IV1

Entities:

Entity 1, IF2 domain III-IV 240 residues - 26759 Da.

Please notice that since residue X is removed from Proline-deletion the numbering is dis-continuous.

1   ASNGLUPHEGLULEUGLYTHRARGGLYSER
2   SERARGVALASPLEUGLNGLUGLNARGSER
3   VALLYSTHRARGVALSERLEUASPASPLEU
4   PHEGLUGLNILELYSGLNGLYGLUMETLYS
5   GLULEUASNLEUILEVALLYSALAASPVAL
6   GLNGLYSERVALGLUALALEUVALALAALA
7   LEUGLNLYSILEASPVALGLUGLYVALARG
8   VALLYSILEILEHISALAALAVALGLYALA
9   ILETHRGLUSERASPILESERLEUALATHR
10   ALASERASNALAILEVALILEGLYPHEASN
11   VALARGPROASPALAASNALALYSARGALA
12   ALAGLUSERGLULYSVALASPILEARGLEU
13   HISARGILEILETYRASNVALILEGLUGLU
14   ILEGLUALAALAMETLYSGLYMETLEUASP
15   GLUTYRGLUGLULYSVALILEGLYGLNALA
16   GLUVALARGGLNTHRPHELYSVALSERLYS
17   VALGLYTHRILEALAGLYCYSTYRVALTHR
18   ASPGLYLYSILETHRARGASPSERLYSVAL
19   ARGLEUILEARGGLNGLYILEVALVALTYR
20   GLUGLYGLUILEASPSERLEULYSARGTYR
21   LYSASPASPVALARGGLUVALALAGLNGLY
22   TYRGLUCYSGLYLEUTHRILELYSASNPHE
23   ASNASPILELYSGLUGLYASPVALILEGLU
24   ALATYRVALMETGLNGLUVALALAARGALA

Samples:

sample_2: domain III-IV, [U-15N], 0.5 mM; potassium phosphate 20 mM; potassium chloride 200 mM; D2O, [U-2H], 10 % (v/v); EDTA-free protease inhibitor; sodium azide 0.02 % (w/v)

sample_1: domain III-IV, [U-13C; U-15N], 0.5 mM; Potassium phosphate 20 mM; potassium chloride 200 mM; D2O, [U-2H], 10 % (v/v); EDTA-free protease inhibitor; sodium azide 0.02 % (w/v)

conditions_1: pH: 5.2; temperature: 307 K

Experiments:

NameSampleSample stateSample conditions
1H15N_HSQCsample_2not availableconditions_1
HNCAsample_1not availableconditions_1
HNCACBsample_1not availableconditions_1
CBCA(CO)NHsample_1not availableconditions_1
NOESY-[15N]-HSQCsample_2not availableconditions_1
R1-1H15N-HSQCsample_2not availableconditions_1
R2-1H15N-CPMGsample_2not availableconditions_1
1H15N-hetNOEsample_2not availableconditions_1

Software:

xwinnmr v3.5, BRUKER - acquisition of NMR spectra

NMRPipe, Frank Delaglio - processing of NMR spectra

NMRView v5.0.3, Bruce A. Johnson - spectral analysis and heteronuclear NOE calculation

CurveFit, A.G. Palmer III - fitting of signal intensities to obtain relaxation rates

NMR spectrometers:

  • Bruker Avance 600.13 MHz

Related Database Links:

BMRB 6577
PDB
DBJ BAD75548 GAD12201 GAJ59418
EMBL CAA27987
GB ACX78663 ADI27260 ADU93636 AEV18768 AGE21726
REF WP_011230763 WP_013145729 WP_013523417 WP_015374430 WP_020959388
SP P04766 Q5L0I8