BMRB Entry 6995

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR6995
MolProbity Validation Chart

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Title:
Solution structure of GDP-bound form of the GTP/GDP binding domain of translation initiation factor IF2
Deposition date:
2006-02-20
Original release date:
2006-11-07
Authors:
Tischenko, Eugene; Folkers, Gert; Boelens, Rolf; Gualerzi, Claudio
Citation:

Citation: Milon, P.; Tischenko, Eugene; Tomsic, J.; Caserta, E.; Folkers, Gert; 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).
PubMed: 16968770

Assembly members:

Assembly members:
IF2G2-GDP, polymer, 178 residues, 19500 Da.
GDP, non-polymer, 443.201 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: recombinant technology

Entity Sequences (FASTA):

Entity Sequences (FASTA):
IF2G2-GDP: GSHMVERPPVVTIMGHVDHG KTTLLDAIRHSKVTEQEAGG ITQHIGAYQVTVNDKKITFL DTPGHEAFTTMRARGAQVTD IVILVVAADDGVMPQTVEAI NHAKAANVPIIVAINKMDKP EANPDRVMQELMEYNLVPEE WGGDTIFCKLSAKTKEGLDH LLEMILLVSEMEELKANP

Data sets:
Data typeCount
13C chemical shifts620
15N chemical shifts142
1H chemical shifts933

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1g2 complexed with GDP1
2GDP2

Entities:

Entity 1, g2 complexed with GDP 178 residues - 19500 Da.

GSHM tag + B.st. IF2(residues 241-415)

1   GLYSERHISMETVALGLUARGPROPROVAL
2   VALTHRILEMETGLYHISVALASPHISGLY
3   LYSTHRTHRLEULEUASPALAILEARGHIS
4   SERLYSVALTHRGLUGLNGLUALAGLYGLY
5   ILETHRGLNHISILEGLYALATYRGLNVAL
6   THRVALASNASPLYSLYSILETHRPHELEU
7   ASPTHRPROGLYHISGLUALAPHETHRTHR
8   METARGALAARGGLYALAGLNVALTHRASP
9   ILEVALILELEUVALVALALAALAASPASP
10   GLYVALMETPROGLNTHRVALGLUALAILE
11   ASNHISALALYSALAALAASNVALPROILE
12   ILEVALALAILEASNLYSMETASPLYSPRO
13   GLUALAASNPROASPARGVALMETGLNGLU
14   LEUMETGLUTYRASNLEUVALPROGLUGLU
15   TRPGLYGLYASPTHRILEPHECYSLYSLEU
16   SERALALYSTHRLYSGLUGLYLEUASPHIS
17   LEULEUGLUMETILELEULEUVALSERGLU
18   METGLUGLULEULYSALAASNPRO

Entity 2, GDP - C10 H15 N5 O11 P2 - 443.201 Da.

1   GDP

Samples:

sample_2: IF2G2, [U-13C; U-15N], 0.6 ± 0.2 mM; potassium phosphate 20 ± 2 mM; potassiumm chloride 150 ± 5 mM; DTT 1 ± 0.1 mM; GDP 1 ± 0.1 mM; MgCl2 5 ± 0.2 mM

conditions_1: pH: 6.5; temperature: 315 K

Experiments:

NameSampleSample stateSample conditions
15N_HSQCsample_2not availableconditions_1
13C_HSQC-CTsample_2not availableconditions_1
13C_HSQC-CT-aromasample_2not availableconditions_1
HNCAsample_2not availableconditions_1
HNCOCAsample_2not availableconditions_1
HNCOsample_2not availableconditions_1
HCCCONH-TOCSYsample_2not availableconditions_1
hCCCONH-TOCSYsample_2not availableconditions_1
hCCH-TOCSYsample_2not availableconditions_1
NOE-15N_HSQCsample_2not availableconditions_1
NOE-13C_HSQCsample_2not availableconditions_1

Software:

xwinnmr v3.0, bruker - NMR data acquisitiuon

nmrPipe/draw, NIH - processing

NMRView v5.0, Merk - spectra analysis

NMR spectrometers:

  • BRUKER AVANCE 600 MHz
  • BRUKER AVANCE 600 MHz
  • BRUKER AVANCE 900 MHz

Related Database Links:

BMRB 6946
PDB
DBJ BAD75548 GAD12201 GAJ59418
EMBL CAA27987
GB ABO66491 ACX78663 ADI27260 ADU93636 AEV18768
REF WP_008878544 WP_011230763 WP_011887154 WP_013145729 WP_013523417
SP A4IMD7 P04766 Q5L0I8
AlphaFold A4IMD7 P04766 Q5L0I8

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks