BMRB Entry 11534

Name: Solution structure of the GGQ domain of YaeJ protein from Escherichia coli
Published: 2013-12-23

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PDB ID: 2rtx
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11534
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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:

Solution structure of the GGQ domain of YaeJ protein from Escherichia coli

Deposition date:

2013-09-21

Original release date:

2013-12-23

Authors:

Nameki, Nobukazu; Enomoto, Mayu; Kogure, Hiroyuki; Tochio, Naoya; Guntert, Peter

Citation:

Citation: Kogure, Hiroyuki; Nameki, Nobukazu. "Identification of residues required for stalled-ribosome rescue in the codon-independent release factor YaeJ" Nucleic Acids Res. ., .-. (2013).
PubMed: 24322300

Assembly members:

Assembly members:
entity, polymer, 121 residues, 13473.514 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: cell free synthesis Host organism: Escherichia coli Vector: not applicable

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: MIVISRHVAIPDGELEITAI RAQGAGGQHVNKTSTAIHLR FDIRASSLPEYYKERLLAAS HHLISSDGVIVIKAQEYRSQ ELNREAALARLVAMIKELTT EKKARRPTRSGPSSGENLYF Q

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	536
15N chemical shifts	123
1H chemical shifts	864

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	the GGQ domain of YaeJ protein	1

Entities:

Entity 1, the GGQ domain of YaeJ protein 121 residues - 13473.514 Da.

Residues 110-121 represent a non-native affinity tag.

1

MET

ILE

VAL

ILE

SER

ARG

HIS

VAL

ALA

ILE

2

PRO

ASP

GLY

GLU

LEU

GLU

ILE

THR

ALA

ILE

3

ARG

ALA

GLN

GLY

ALA

GLY

GLN

HIS

VAL

4

ASN

LYS

THR

SER

THR

ALA

ILE

HIS

LEU

ARG

5

PHE

ASP

ILE

ARG

ALA

SER

LEU

PRO

GLU

6

TYR

LYS

GLU

ARG

LEU

ALA

SER

7

HIS

LEU

ILE

SER

ASP

GLY

VAL

ILE

8

VAL

ILE

LYS

ALA

GLN

GLU

TYR

ARG

SER

GLN

9

GLU

LEU

ASN

ARG

GLU

ALA

LEU

ALA

ARG

10

LEU

VAL

ALA

MET

ILE

LYS

GLU

LEU

THR

11

GLU

LYS

ALA

ARG

PRO

THR

ARG

SER

12

GLY

PRO

SER

GLY

GLU

ASN

LEU

TYR

PHE

13

GLN

Samples:

sample_1: GGQ domain, [U-13C; U-15N], 1 mM; TRIS, [U-2H], 20 mM; NaCl 100 mM; DTT, [U-2H], 1 mM; NaN3 0.02%; H2O, [U-2H], 90%; D2O 10%

sample_conditions_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1

Software:

CYANA v3.93, Guntert et al. - structure solution

xwinnmr, Bruker Biospin - collection

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

OPALp v1.4, Koradi, Guntert, Billeter - refinement

Kujira, Kobayashi, N. - data analysis

NMRView, Johnson, One Moon Scientific - data analysis

NMR spectrometers:

Bruker Avance 700 MHz

PDB	2RTX
DBJ	BAI29068
EMBL	CSE40362 CSE41074 CSE45877 CSE47218 CSE48511
GB	EFZ51677 EGX13540 EIQ48412 EIQ48742 EIQ55363
REF	WP_000635548