BMRB Entry 16001

Name: SOLUTION STRUCTURE OF DNA BINDING DOMAIN OF E. COLI ARAC
Published: 2008-11-07

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PDB ID: 2k9s
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16001
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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 DNA BINDING DOMAIN OF E. COLI ARAC

Deposition date:

2008-10-23

Original release date:

2008-11-07

Authors:

Rodgers, Michael; Schleif, Robert

Citation:

Citation: Rodgers, Michael; Schleif, Robert. "Solution Structure of the DNA binding domain of AraC protein" Proteins 77, 202-208 (2009).
PubMed: 19422057

Assembly members:

Assembly members:
AraC-DBD, polymer, 107 residues, 12096.795 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: pET24d

Entity Sequences (FASTA):

Entity Sequences (FASTA):
AraC-DBD: MDNRVREACQYISDHLADSN FDIASVAQHVCLSPSRLSHL FRQQLGISVLSWREDQRISQ AKLLLSTTRMPIATVGRNVG FDDQLYFSRVFKKCTGASPS EFRAGCE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	465
15N chemical shifts	114
1H chemical shifts	715

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	AraC-DBD	1

Entities:

Entity 1, AraC-DBD 107 residues - 12096.795 Da.

Residues 175 through 280 of native E. coli AraC

1

MET

ASP

ASN

ARG

VAL

ARG

GLU

ALA

CYS

GLN

2

TYR

ILE

SER

ASP

HIS

LEU

ALA

ASP

SER

ASN

3

PHE

ASP

ILE

ALA

SER

VAL

ALA

GLN

HIS

VAL

4

CYS

LEU

SER

PRO

SER

ARG

LEU

SER

HIS

LEU

5

PHE

ARG

GLN

LEU

GLY

ILE

SER

VAL

LEU

6

SER

TRP

ARG

GLU

ASP

GLN

ARG

ILE

SER

GLN

7

ALA

LYS

LEU

SER

THR

ARG

MET

8

PRO

ILE

ALA

THR

VAL

GLY

ARG

ASN

VAL

GLY

9

PHE

ASP

GLN

LEU

TYR

PHE

SER

ARG

VAL

10

PHE

LYS

CYS

THR

GLY

ALA

SER

PRO

SER

11

GLU

PHE

ARG

ALA

GLY

CYS

GLU

Samples:

AraC-DBD-1: AraC-DBD, [U-100% 15N], 0.5 – 1.0 mM; PHOSPHATE BUFFER 50 mM; NACL 400 mM; NAN3 0.1 mM

AraC-DBD-2: AraC-DBD, [U-100% 13C; U-100% 15N], 0.5-1.0 mM; PHOSPHATE BUFFER 50 mM; NACL 400 mM; NAN3 0.1 mM

sample_conditions_1: ionic strength: 400 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D_13C-SEPARATED_ALI_NOESY	AraC-DBD-2	isotropic	sample_conditions_1
3D_13C-SEPARATED_ARO_NOESY	AraC-DBD-2	isotropic	sample_conditions_1
3D 1H-15N-SEPARATED NOESY	AraC-DBD-1	isotropic	sample_conditions_1
2D 1H-15N HSQC	AraC-DBD-1	isotropic	sample_conditions_1
2D 1H-13C HSQC	AraC-DBD-2	isotropic	sample_conditions_1
3D HNCO	AraC-DBD-2	isotropic	sample_conditions_1
3D HNCA	AraC-DBD-2	isotropic	sample_conditions_1
3D HNCACB	AraC-DBD-2	isotropic	sample_conditions_1
3D HN(CO)CA	AraC-DBD-2	isotropic	sample_conditions_1
3D CBCA(CO)NH	AraC-DBD-2	isotropic	sample_conditions_1
3D HCCH-COSY	AraC-DBD-2	isotropic	sample_conditions_1
3D HCCCONH-TOCSY	AraC-DBD-2	isotropic	sample_conditions_1
3D H_CCCONH-TOCSY	AraC-DBD-2	isotropic	sample_conditions_1

Software:

CYANA v2.0, P.GUNTERT ET AL. - refinement

ATHNOS-CANDID, Herrmann, Guntert and Wuthrich - structure solution

TALOS, Cornilescu, Delaglio and Bax - structure solution

NMR spectrometers:

VARIAN INOVA 800 MHz
Bruker Avance 600 MHz
Varian INOVA 500 MHz
Varian INOVA 600 MHz

PDB	2K9S
DBJ	BAB33491 BAB96633 BAG75588 BAI23427 BAI28943
EMBL	CAA23507 CAA23508 CAL59724 CAP74634 CAQ30582
GB	AAA23092 AAA23466 AAA27026 AAC53662 AAC73175
REF	NP_308095 NP_414606 NP_459109 NP_706017 WP_000840169
SP	P03022 P0A9E0 P0A9E1 P11765
AlphaFold	P03022 P0A9E0 P0A9E1 P11765