BMRB Entry 15691

Name: Structure of the DBD domain of E. coli antitoxin RelB
Published: 2008-06-27

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PDB ID: 2k29
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15691
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structure of the DBD domain of E. coli antitoxin RelB

Deposition date:

2008-03-23

Original release date:

2008-06-27

Authors:

Li, Guang-Yao; Zhang, Yonglong; Inouye, Masayori; Ikura, Mitsuhiko

Citation:

Citation: Li, Guang-Yao; Zhang, Yonglong; Inouye, Masayori; Ikura, Mitsuhiko. "Structural mechanism of transcriptional autorepression of the Escherichia coli RelB/RelE antitoxin/toxin module" J. Mol. Biol. 380, 107-119 (2008).
PubMed: 18501926

Assembly members:

Assembly members:
RelB, polymer, 53 residues, 5993.9 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: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RelB: GSHMGSINLRIDDELKARSY AALEKMGVTPSEALRLMLEY IADNERLPFKQTL

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
RDCs
- RDC_list_1

Data type	Count
15N chemical shifts	52
1H chemical shifts	362
residual dipolar couplings	42

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 53 residues - 5993.9 Da.

Residues 1-3 represent a non-native affinity tag. This is a DNA binding domain of a antitoxin protein.

1

GLY

SER

HIS

MET

GLY

SER

ILE

ASN

LEU

ARG

2

ILE

ASP

GLU

LEU

LYS

ALA

ARG

SER

TYR

3

ALA

LEU

GLU

LYS

MET

GLY

VAL

THR

PRO

4

SER

GLU

ALA

LEU

ARG

LEU

MET

LEU

GLU

TYR

5

ILE

ALA

ASP

ASN

GLU

ARG

LEU

PRO

PHE

LYS

6

GLN

THR

LEU

Samples:

sample_1: RelBN, [U-100% 13C; U-100% 15N], 0.5-1.0 mM; sodium phosphate 20 mM; sodium chloride 100 mM; DTT 1 mM; sodium azide 1 uM

sample_2: RelBN, [U-100% 13C; U-100% 15N], 0.5-1.0 mM; sodium phosphate 20 mM; sodium chloride 100 mM; DTT 1 mM; sodium azide 1 uM

sample_conditions_1: ionic strength: 0.12 M; pH: 7.0; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	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

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

VNMR v6.1C, Varian - collection

XEASY, Bartels et al. - chemical shift assignment

NMR spectrometers:

Varian INOVA 600 MHz

PDB	2K29 4FXE
DBJ	BAA15263 BAI25453 BAJ43364 BAN94923
EMBL	CAA26250 CAQ98463 CBG34538 CBK86917 CCF87937
GB	AAC74637 AAN43138 AAP17029 AAS76441 ABF03723
REF	NP_416082 NP_707431 WP_000534857 WP_000534858 WP_001408098
SP	P0C079 P0C080
AlphaFold	P0C079 P0C080