BMRB Entry 11555

Name: Structure of the YAM domain of E. coli Transporter YajR
Published: 2014-06-30

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PDB ID: 2ru9
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11555
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structure of the YAM domain of E. coli Transporter YajR

Deposition date:

2014-02-27

Original release date:

2014-06-30

Authors:

Liu, Xuehui; Feng, Wei

Citation:

Citation: Jiang, Daohua; Zhang, Xuejun. "Atomic Resolution Structure of the E. coli YajR Transporter YAM Domain" Biochem. Biophys. Res. Commun. ., .-..
PubMed: 24952155

Assembly members:

Assembly members:
entity, polymer, 76 residues, 7876.034 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: pET-28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: MGKEPPYVSSLRIEIPADIA ANEALKVRLLETEGVKEVLI AEEEHSAYVKIDSKVTNRFE VEQAIRQALEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	285
15N chemical shifts	68
1H chemical shifts	458

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity	1

Entities:

Entity 1, entity 76 residues - 7876.034 Da.

1

MET

GLY

LYS

GLU

PRO

TYR

VAL

SER

2

LEU

ARG

ILE

GLU

ILE

PRO

ALA

ASP

ILE

ALA

3

ALA

ASN

GLU

ALA

LEU

LYS

VAL

ARG

LEU

4

GLU

THR

GLU

GLY

VAL

LYS

GLU

VAL

LEU

ILE

5

ALA

GLU

HIS

SER

ALA

TYR

VAL

LYS

6

ILE

ASP

SER

LYS

VAL

THR

ASN

ARG

PHE

GLU

7

VAL

GLU

GLN

ALA

ILE

ARG

GLN

ALA

LEU

GLU

8

HIS

Samples:

sample_1: YAM 1.2 mM; H2O 90%; D2O 10%; sodium phosphate 50 mM; EDTA 1 mM; DTT 1 mM; sodium chloride 150 mM

sample_conditions_1: ionic strength: 0.2 M; pH: 6.3; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	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

Software:

ARIA v2.3, Linge, O'Donoghue and Nilges - chemical shift assignment, structure solution

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

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

NMR spectrometers:

Varian INOVA 600 MHz

PDB	2RU9 3WDO 4Q2L 4Q2M
DBJ	BAG75973 BAI23798 BAI29269 BAI34436 BAI53927
EMBL	CAP74961 CAQ30896 CAQ90093 CAQ97299 CAR01770
GB	AAN79016 AAZ87180 ABB60522 ABE05951 ABG68516
REF	WP_001000941 WP_001000945 WP_001000947 WP_001000948 WP_001000951