Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR53588

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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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Name: YdbL in complex with C-terminal peptide of YnbE from Escherichia coli
Published: 2026-06-16

Title:

YdbL in complex with C-terminal peptide of YnbE from Escherichia coli

Deposition date:

2026-02-26

Original release date:

2026-06-16

Authors:

De'Ath, Clare; Redfield, Christina; Isom, Georgia

Citation:

Citation: De'Ath, Clare; Redfield, Christina; Isom, Georgia. "1H, 13C and 15N resonance assignments for YdbL from Escherichia coli in both its apo state and in complex with the C-terminus of YnbE." mBio ., .-..

Assembly members:

Assembly members:
entity_1, polymer, 88 residues, Formula weight is not available
entity_2, polymer, 23 residues, Formula weight is not available

Natural source:

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

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GLTLDEARTQGRVGETFYGY LVALKTDAETEKLVADINAE RKASYQQLAKQNNVSVDDIA KLAGQKLVARAKPGEYVQGI NGKWVRKF
entity_2: EHEIIIKADKDVEELLETRS DLF

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	331
15N chemical shifts	97
1H chemical shifts	534

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	YdbL	1
2	YnbE	2

Entities:

Entity 1, YdbL 88 residues - Formula weight is not available

Residue 21 G is leftover from TEV cleavage site. Mature protein sequence for YdbL begins from residue 22 i.e., LTLDEARTQGRVGETFYGYLVALKTDAETEKLVADINAERKASYQQLAKQNNVSVDDIAKLAGQKLVARAKPGEYVQGINGKWVRKF after signal peptide cleavage.

1

GLY

LEU

THR

LEU

ASP

GLU

ALA

ARG

THR

GLN

2

GLY

ARG

VAL

GLY

GLU

THR

PHE

TYR

GLY

TYR

3

LEU

VAL

ALA

LEU

LYS

THR

ASP

ALA

GLU

THR

4

GLU

LYS

LEU

VAL

ALA

ASP

ILE

ASN

ALA

GLU

5

ARG

LYS

ALA

SER

TYR

GLN

LEU

ALA

LYS

6

GLN

ASN

VAL

SER

VAL

ASP

ILE

ALA

7

LYS

LEU

ALA

GLY

GLN

LYS

LEU

VAL

ALA

ARG

8

ALA

LYS

PRO

GLY

GLU

TYR

VAL

GLN

GLY

ILE

9

ASN

GLY

LYS

TRP

VAL

ARG

LYS

PHE

Entity 2, YnbE 23 residues - Formula weight is not available

Peptide synthesised of residues 39-61 from YnbE.

1

GLU

HIS

GLU

ILE

LYS

ALA

ASP

LYS

2

ASP

VAL

GLU

LEU

GLU

THR

ARG

SER

3

ASP

LEU

PHE

Samples:

sample_1: YdbL, [U-100% 15N], 180 uM; sodium phosphate 10 mM; sodium chloride 20 mM; D2O 5%; H2O 95%; YnbE 180 uM

sample_2: YdbL, [U-100% 13C; U-100% 15N], 60 uM; sodium phosphate 10 mM; sodium chloride 20 mM; D2O, [U-100% 2H], 5%; H2O 95%; YnbE 60 uM

sample_conditions_1: ionic strength: 44.3 mM; pH: 7.4; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N BEST TROSY	sample_1	isotropic	sample_conditions_1
3D 15N-edited NOESY HSQC	sample_2	isotropic	sample_conditions_1
3D 15N-edited TOCSY HSQC	sample_2	isotropic	sample_conditions_1
(H)CC(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1

Software:

Bruker TopSpin v3.2 - collection

NMRPipe - processing

CcpNMR v2.5.2 - chemical shift assignment

istHMS vhmsIST_v211_64b - processing

NMR spectrometers:

Bruker AVANCE III 750 MHz
Bruker AVANCE III 950 MHz

BMRB Entry 53588