BMRB Entry 19946

Name: 3D NMR structure of the cytoplasmic rhodanese domain of the full-length inner membrane protein YgaP from Escherichia coli
Published: 2014-06-23

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PDB ID: 2mol
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19946
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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 cytoplasmic rhodanese domain of the full-length inner membrane protein YgaP from Escherichia coli

Deposition date:

2014-04-27

Original release date:

2014-06-23

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:
YgaP, polymer, 108 residues, 11716.429 Da.

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: pET3a-LIC

Entity Sequences (FASTA):

Entity Sequences (FASTA):
YgaP: ALTTISPHDAQELIARGAKL IDIRDADEYLREHIPEADLA PLSVLEQSGLPAKLRHEQII FHCQAGKRTSNNADKLAAIA APAEIFLLEDGIDGWKKAGL PVAVNKSQ

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	698
13C chemical shifts	303
15N chemical shifts	112

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	YgaP	1

Entities:

Entity 1, YgaP 108 residues - 11716.429 Da.

1

ALA

LEU

THR

ILE

SER

PRO

HIS

ASP

ALA

2

GLN

GLU

LEU

ILE

ALA

ARG

GLY

ALA

LYS

LEU

3

ILE

ASP

ILE

ARG

ASP

ALA

ASP

GLU

TYR

LEU

4

ARG

GLU

HIS

ILE

PRO

GLU

ALA

ASP

LEU

ALA

5

PRO

LEU

SER

VAL

LEU

GLU

GLN

SER

GLY

LEU

6

PRO

ALA

LYS

LEU

ARG

HIS

GLU

GLN

ILE

7

PHE

HIS

CYS

GLN

ALA

GLY

LYS

ARG

THR

SER

8

ASN

ALA

ASP

LYS

LEU

ALA

ILE

ALA

9

ALA

PRO

ALA

GLU

ILE

PHE

LEU

GLU

ASP

10

GLY

ILE

ASP

GLY

TRP

LYS

ALA

GLY

LEU

11

PRO

VAL

ALA

VAL

ASN

LYS

SER

GLN

Samples:

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

sample_2: YgaP, [U-100% 13C; U-100% 15N; U-80% 2H], 0.5 mM; H2O 95%; D2O, [U-100% 2H], 5%

sample_conditions_1: 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_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HN(CO)CA	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

XEASY, Bartels et al. - chemical shift assignment

NMR spectrometers:

Bruker Avance 700 MHz

BMRB	17137 19943 25085
PDB	2MOI 2MOL 2MRM
DBJ	BAB36952 BAE76780 BAG78445 BAI26930 BAI31960
EMBL	CAP77107 CAQ33005 CAQ87965 CAQ99590 CAR04179
GB	AAC75715 AAG57776 AAN44189 AAN81669 AAP18017
REF	NP_311556 NP_417154 NP_708482 WP_001229433 WP_001229436
SP	P55734
AlphaFold	P55734