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 15304

Title: NMR strcuture determination of the periplasmic domain of ExbD from E.coli   PubMed: 17927700

Deposition date: 2007-06-14 Original release date: 2008-02-28

Authors: Garcia-Herrero, A.; Peacock, S.; Howard, P.; Vogel, H.

Citation: Garcia-Herrero, A.; Peacock, S.; Howard, P.; Vogel, H.. "The solution structure of the periplasmic domain of the TonB system ExbD protein reveals an unexpected structural homology with siderophore binding proteins."  Mol. Microbiol. 66, 872-889 (2007).

Assembly members:
Biopolymer_transport_exbD_protein, polymer, 99 residues, Formula weight is not available

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Eubacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
Biopolymer_transport_exbD_protein: MDVKVNLPASTSTPQPRPEK PVYLSVKADNSMFIGNDPVT DETMITALNALTEGKKDTTI FFRADKTVDYETLMKVMDTL HQAGYLKIGLVGEETAKAK

Data sets:
Data typeCount
13C chemical shifts411
15N chemical shifts94
1H chemical shifts693

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1ExbD periplasmic domain1

Entities:

Entity 1, ExbD periplasmic domain 99 residues - Formula weight is not available

1   METASPVALLYSVALASNLEUPROALASER
2   THRSERTHRPROGLNPROARGPROGLULYS
3   PROVALTYRLEUSERVALLYSALAASPASN
4   SERMETPHEILEGLYASNASPPROVALTHR
5   ASPGLUTHRMETILETHRALALEUASNALA
6   LEUTHRGLUGLYLYSLYSASPTHRTHRILE
7   PHEPHEARGALAASPLYSTHRVALASPTYR
8   GLUTHRLEUMETLYSVALMETASPTHRLEU
9   HISGLNALAGLYTYRLEULYSILEGLYLEU
10   VALGLYGLUGLUTHRALALYSALALYS

Samples:

sample_1: Biopolymer transport exbD protein, [U-13C; U-15N], 0.2 mM; D2O 100%

sample_2: Biopolymer transport exbD protein, [U-15N], 0.2 mM; D2O 10%; H2O 90%

sample_3: Biopolymer transport exbD protein 0.2 mM; D2O 100%

sample_conditions_1: pH: 3; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D 13C-separated NOESYsample_1isotropicsample_conditions_1
3D 15N-separated NOESYsample_2isotropicsample_conditions_1
2D NOESYsample_3isotropicsample_conditions_1

Software:

CYANA v2.0, GUNTERT, P. ET AL. - refinement

NMR spectrometers:

  • Bruker AVANCE 500 MHz
  • Bruker AVANCE 700 MHz

Related Database Links:

PDB
DBJ BAB37312 BAE77063 BAG78813 BAI27294 BAI32408
EMBL CAP77468 CAQ33346 CAQ90439 CAQ99968 CAR04618
GB AAA23733 AAA69172 AAC76041 AAG58141 AAN44528
REF NP_311916 NP_417478 NP_708821 WP_001062147 WP_001240704
SP P0ABV2 P0ABV3 P0ABV4 P0ABV5

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts