BMRB Entry 15304

Name: NMR strcuture determination of the periplasmic domain of ExbD from E.coli
Published: 2008-02-28

Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15304

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR strcuture determination of the periplasmic domain of ExbD from E.coli

Deposition date:

2007-06-14

Original release date:

2008-02-28

Authors:

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

Citation:

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).
PubMed: 17927700

Assembly members:

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

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET30a

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	411
15N chemical shifts	94
1H chemical shifts	693

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	ExbD periplasmic domain	1

Entities:

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

1

MET

ASP

VAL

LYS

VAL

ASN

LEU

PRO

ALA

SER

2

THR

SER

THR

PRO

GLN

PRO

ARG

PRO

GLU

LYS

3

PRO

VAL

TYR

LEU

SER

VAL

LYS

ALA

ASP

ASN

4

SER

MET

PHE

ILE

GLY

ASN

ASP

PRO

VAL

THR

5

ASP

GLU

THR

MET

ILE

THR

ALA

LEU

ASN

ALA

6

LEU

THR

GLU

GLY

LYS

ASP

THR

ILE

7

PHE

ARG

ALA

ASP

LYS

THR

VAL

ASP

TYR

8

GLU

THR

LEU

MET

LYS

VAL

MET

ASP

THR

LEU

9

HIS

GLN

ALA

GLY

TYR

LEU

LYS

ILE

GLY

LEU

10

VAL

GLY

GLU

THR

ALA

LYS

ALA

LYS

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:

Name	Sample	Sample state	Sample conditions
3D 13C-separated NOESY	sample_1	isotropic	sample_conditions_1
3D 15N-separated NOESY	sample_2	isotropic	sample_conditions_1
2D NOESY	sample_3	isotropic	sample_conditions_1

Software:

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

NMR spectrometers:

Bruker AVANCE 500 MHz
Bruker AVANCE 700 MHz

PDB	2PFU
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
AlphaFold	P0ABV2 P0ABV3 P0ABV4 P0ABV5