BMRB Entry 34826

Name: Structure of the dimeric, periplasmic domain of ExbD
Published: 2023-10-31

Click here to enlarge.

PDB ID: 8pek
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34826
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

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

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

Structure of the dimeric, periplasmic domain of ExbD

Deposition date:

2023-06-14

Original release date:

2023-10-31

Authors:

Zinke, M.; Bardiaux, B.; Izadi-Pruneyre, N.

Citation:

Citation: Zinke, M.; Lejeune, M.; Mechaly, A.; Bardiaux, B.; Boneca, I.; Delepelaire, P.; Izadi-Pruneyre, N.. "Ton Motor Conformational Switch and Peptidoglycan Role in Bacterial Nutrient Uptake." Biorxiv ., .-. (2023).
PubMed: 37609138

Assembly members:

Assembly members:
entity_1, polymer, 99 residues, 10870.383 Da.

Natural source:

Natural source: Common Name: Serratia marcescens Taxonomy ID: 615 Superkingdom: Bacteria Kingdom: not available Genus/species: Serratia marcescens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3) Vector: pet30(a)+

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SVDIRVDLPASSAKPQPRPE KPVFLSVKADKQLYVGDQPV NADQLTSVLDQRTQANKETT IFFQADKSVDYETLMSVMDT LRKAGYLKVGLVGMEGAAK

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	876
15N chemical shifts	198
1H chemical shifts	1394

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	1

Entities:

Entity 1, unit_1 99 residues - 10870.383 Da.

1

SER

VAL

ASP

ILE

ARG

VAL

ASP

LEU

PRO

ALA

2

SER

ALA

LYS

PRO

GLN

PRO

ARG

PRO

GLU

3

LYS

PRO

VAL

PHE

LEU

SER

VAL

LYS

ALA

ASP

4

LYS

GLN

LEU

TYR

VAL

GLY

ASP

GLN

PRO

VAL

5

ASN

ALA

ASP

GLN

LEU

THR

SER

VAL

LEU

ASP

6

GLN

ARG

THR

GLN

ALA

ASN

LYS

GLU

THR

7

ILE

PHE

GLN

ALA

ASP

LYS

SER

VAL

ASP

8

TYR

GLU

THR

LEU

MET

SER

VAL

MET

ASP

THR

9

LEU

ARG

LYS

ALA

GLY

TYR

LEU

LYS

VAL

GLY

10

LEU

VAL

GLY

MET

GLU

GLY

ALA

LYS

Samples:

sample_1: sodium phosphate 50 mM; sodium chloride 50 mM; periplasmic domain of ExbD from Serratia marcescens, [U-100% 13C; U-100% 15N], 1.5 mM

sample_2: sodium phosphate 50 mM; sodium chloride 50 mM; periplasmic domain of ExbD from Serratia marcescens, [U-100% 13C; U-100% 15N], 1.5 mM

sample_3: sodium phosphate 50 mM; sodium chloride 50 mM; periplasmic domain of ExbD from Serratia marcescens, [U-100% 13C; U-100% 15N; U-95% 2H], 2 mM

sample_4: sodium phosphate 50 mM; sodium chloride 50 mM; periplasmic domain of ExbD from Serratia marcescens, [U-100% 13C; U-100% 15N; U-95% 2H; natural abundance], 2 mM

sample_conditions_1: ionic strength: 0.3 mM; pH: 7; pressure: 1 atm; temperature: 293.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(COCA)CB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
2D hbCBcgcdHD	sample_1	isotropic	sample_conditions_1
2D hbCBcgcdceHE	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
3D HNCO hydrogen bond detection	sample_3	isotropic	sample_conditions_1
3D DOUBLY-FILTERED 1H-13C NOESY	sample_4	isotropic	sample_conditions_1
3D DOUBLY-FILTERED 1H-15N NOESY	sample_4	isotropic	sample_conditions_1

Software:

CcpNmr Analysis Assign v3.1, Skinner SP, Fogh RH, Boucher W, Ragan TJ, Mureddu LG, and Vuister GW - chemical shift assignment

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

ARIA v2.3.3, Linge, O'Donoghue and Nilges - structure calculation

CcpNmr Analysis v2.5, Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, and Laue ED - peak picking

NMRPipe v10.9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

TALOS-N v4.12, Shen and Bax - data analysis

NMR spectrometers:

Bruker AVANCE NEO 800 MHz
Bruker AVANCE III HD 600 MHz

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