BMRB Entry 15378

Name: NMR structure of the S. aureus VraR DNA binding domain
Published: 2008-03-13

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15378

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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:

NMR structure of the S. aureus VraR DNA binding domain

Deposition date:

2007-07-13

Original release date:

2008-03-13

Authors:

Donaldson, Logan

Citation:

Citation: Donaldson, Logan. "The NMR Structure of the Staphylococcus aureus Response Regulator VraR DNA Binding Domain Reveals a Dynamic Relationship between It and Its Associated Receiver Domain" Biochemistry 47, 3379-3388 (2008).
PubMed: 18293926

Assembly members:

Assembly members:
VraR, polymer, 93 residues, 10625.2 Da.

Natural source:

Natural source: Common Name: Staphylococcus aureus Taxonomy ID: 1280 Superkingdom: Bacteria Kingdom: not available Genus/species: Staphylococcus aureus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
VraR: GSSHHHHHHSSGLVPRGSHM KKRAELELYEMLTEREMEIL LLIAKGYSNQEIASASHITI KTVKTHVSNILSKLEVQDRT QAVIYAFQHNLIQ

Data sets:

assigned_chemical_shifts
- assignments_vrar

Data type	Count
13C chemical shifts	239
15N chemical shifts	55
1H chemical shifts	366

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	VraR	1

Entities:

Entity 1, VraR 93 residues - 10625.2 Da.

The first 20 residues are a His6 affinity tag and thrombin protease recognition site derived from pET15b (Novagen). The next 6 residues are derived from the native protein but not included in the structure determination

1

GLY

SER

HIS

SER

2

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

MET

3

LYS

ARG

ALA

GLU

LEU

GLU

LEU

TYR

GLU

4

MET

LEU

THR

GLU

ARG

GLU

MET

GLU

ILE

LEU

5

LEU

ILE

ALA

LYS

GLY

TYR

SER

ASN

GLN

6

GLU

ILE

ALA

SER

ALA

SER

HIS

ILE

THR

ILE

7

LYS

THR

VAL

LYS

THR

HIS

VAL

SER

ASN

ILE

8

LEU

SER

LYS

LEU

GLU

VAL

GLN

ASP

ARG

THR

9

GLN

ALA

VAL

ILE

TYR

ALA

PHE

GLN

HIS

ASN

10

LEU

ILE

GLN

Samples:

sample_1: VraR, [U-98% 15N], 0.3 mM; NaCl 750 mM; H2O 90%; D2O 10%

sample_2: VraR, [U-98% 13C; U-98% 15N], 0.3 mM; NaCl 750 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 750 mM; pH: 7.8; pressure: 1 atm; temperature: 308.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	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 HNCACB	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
2D (HB)CB(CGCD)HD	sample_1	isotropic	sample_conditions_1
2D (HB)CB(CGCDCE)HE	sample_1	isotropic	sample_conditions_1

Software:

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

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

X-PLOR NIH v2.17, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMRView v5, Johnson, One Moon Scientific - data analysis

NMR spectrometers:

Varian NMRS 600 MHz

GB	14247656 47208328 EUS58931
BMRB	11024
PDB	2RNJ