BMRB Entry 17830

Name: 1H, 13C and 15N Resonance Assignments for Oxidised and Reduced nDsbD fromm Escherichia coli
Published: 2011-10-25

Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17830

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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:

1H, 13C and 15N Resonance Assignments for Oxidised and Reduced nDsbD fromm Escherichia coli

Deposition date:

2011-08-04

Original release date:

2011-10-25

Authors:

Mavridou, Despoina; Stelzl, Lukas; Ferguson, Stuart; Redfield, Christina

Citation:

Citation: Mavridou, Despoina; Saridakis, Emmanuel; Kritsiligkou, Paraskevi; Goddard, Alan; Stevens, Julie; Ferguson, Stuart; Redfield, Christina. "Oxidation state-dependent protein-protein interactions in disulfide cascades." J. Biol. Chem. 286, 24943-24956 (2011).
PubMed: 21543317

Assembly members:

Assembly members:
nDsbD-red, polymer, 139 residues, 15604.5 Da.

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: pET22b(+)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
nDsbD-red: MDTLFDAPGRSQFVPADQAF AFDFQQNQHDLNLTWQIKDG YYLYRKQIRITPEHAKIADV QLPQGVWHEDEFYGKSEIYR DRLTLPVTINQASAGATLTV TYQGCADAGFCYPPETKTVP LSEVVANNAAPQPVGLVPR

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	489
15N chemical shifts	122
1H chemical shifts	763

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	nDsbD-red	1

Entities:

Entity 1, nDsbD-red 139 residues - 15604.5 Da.

Residues L2-V132 of the native sequence have been deposited. This is the N-terminal periplasmic domain of a membrane protein. The N-terminal residues MDT are a result of the cloning process. Residues G133-R137 remain after thrombin cleavage of the affinity tag.

1

MET

ASP

THR

LEU

PHE

ASP

ALA

PRO

GLY

ARG

2

SER

GLN

PHE

VAL

PRO

ALA

ASP

GLN

ALA

PHE

3

ALA

PHE

ASP

PHE

GLN

ASN

GLN

HIS

ASP

4

LEU

ASN

LEU

THR

TRP

GLN

ILE

LYS

ASP

GLY

5

TYR

LEU

TYR

ARG

LYS

GLN

ILE

ARG

ILE

6

THR

PRO

GLU

HIS

ALA

LYS

ILE

ALA

ASP

VAL

7

GLN

LEU

PRO

GLN

GLY

VAL

TRP

HIS

GLU

ASP

8

GLU

PHE

TYR

GLY

LYS

SER

GLU

ILE

TYR

ARG

9

ASP

ARG

LEU

THR

LEU

PRO

VAL

THR

ILE

ASN

10

GLN

ALA

SER

ALA

GLY

ALA

THR

LEU

THR

VAL

11

THR

TYR

GLN

GLY

CYS

ALA

ASP

ALA

GLY

PHE

12

CYS

TYR

PRO

GLU

THR

LYS

THR

VAL

PRO

13

LEU

SER

GLU

VAL

ALA

ASN

ALA

14

PRO

GLN

PRO

VAL

GLY

LEU

VAL

PRO

ARG

Samples:

sample_1: nDsbD-red, [U-98% 15N], 0.5 – 1.0 mM; DTT 20 mM; D2O 5%; H2O 95%

sample_2: nDsbD-red, [U-98% 13C; U-98% 15N], 0.5 – 1.0 mM; DTT 20 mM; D2O 5%; H2O 95%

sample_conditions_1: ionic strength: 0 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC NH2 only	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
3D HN(CA)CO	sample_2	isotropic	sample_conditions_1
3D 1H-15N HSQC-NOESY-HSQC	sample_1	isotropic	sample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CcpNMR, CCPN - chemical shift assignment

NMR spectrometers:

home-built home-built using GE Omega software 750 MHz
Bruker Avance 500 MHz

BMRB	17831
PDB	1JPE 1JZD 1L6P 1VRS 1Z5Y 3PFU
DBJ	BAB38540 BAE78138 BAG66862 BAG79959 BAI28440
EMBL	CAA54781 CAA85375 CAQ34485 CAR01112 CAR05872
GB	AAA97035 AAC77096 AAG59335 AAN45708 AAN83640
REF	NP_313144 NP_418559 NP_710001 WP_000068901 WP_000068902
SP	P36655 P58162 Q0SXE3 Q0T9Q5 Q1R3C4
AlphaFold	P36655 P58162 Q0SXE3 Q0T9Q5 Q1R3C4