BMRB Entry 19994

Name: 3D NMR structure of the transmembrane domain of the full-length inner membrane protein YgaP from Escherichia coli
Published: 2014-09-10

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PDB ID: 2mpn
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR19994
MolProbity Validation Chart

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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:

3D NMR structure of the transmembrane domain of the full-length inner membrane protein YgaP from Escherichia coli

Deposition date:

2014-05-29

Original release date:

2014-09-10

Authors:

Eichmann, Cedric; Tzitzilonis, Christos; Bordignon, Enrica; Maslennikov, Innokentiy; Choe, Senyon; Riek, Roland

Citation:

Citation: Eichmann, Cedric; Tzitzilonis, Christos; Bordignon, Enrica; Maslennikov, Innokentiy; Choe, Senyon; Riek, Roland. "Solution NMR Structure and Functional Analysis of the Integral Membrane Protein YgaP from Escherichia coli." J. Biol. Chem. 289, 23482-23503 (2014).
PubMed: 24958726

Assembly members:

Assembly members:
entity, polymer, 68 residues, 7157.559 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 83333 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET3a-LIC

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: KSQPLPLMRQVQIAAGGLIL IGVVLGYTVNSGFFLLSGFV GAGLLFAGISGFSGMARLLD KMPWNQRA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	298
15N chemical shifts	61
13C chemical shifts	12

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	1

Entities:

Entity 1, entity_1 68 residues - 7157.559 Da.

1

LYS

SER

GLN

PRO

LEU

PRO

LEU

MET

ARG

GLN

2

VAL

GLN

ILE

ALA

GLY

LEU

ILE

LEU

3

ILE

GLY

VAL

LEU

GLY

TYR

THR

VAL

ASN

4

SER

GLY

PHE

LEU

SER

GLY

PHE

VAL

5

GLY

ALA

GLY

LEU

PHE

ALA

GLY

ILE

SER

6

GLY

PHE

SER

GLY

MET

ALA

ARG

LEU

ASP

7

LYS

MET

PRO

TRP

ASN

GLN

ARG

ALA

Samples:

sample_1: entity, [U-100% 13C; U-100% 15N; U-80% 2H], 0.5 mM; H2O 95%; D2O 5%

sample_2: entity, [U-100% 13C; U-100% 15N], 0.5 mM; H2O 95%; D2O 5%

sample_conditions_1: temperature: 273 K; pH: 7.0; pressure: 1 atm; ionic strength: 0 M

sample_conditions_2: temperature: 273 K; pH: 7.0; pressure: 1 atm; ionic strength: 0 M

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_2
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_2
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_2

Software:

XEASY, Bartels et al. - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

Bruker Avance 700 MHz

PDB	2MPN
DBJ	BAB36952 BAE76780 BAG78445 BAI26930 BAI31960
EMBL	CAP77107 CAQ33005 CAQ99590 CAR04179 CAR09287
GB	AAC75715 AAG57776 AAN44189 AAN81669 AAP18017
REF	NP_311556 NP_417154 NP_708482 WP_001229436 WP_001229438
SP	P55734
AlphaFold	P55734