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BMRB: 15378

NMR structure of the S. aureus VraR DNA binding domain

Authors

Donaldson, L.W.

Assembly

VraR

Entity

1. VraR (polymer, Thiol state: all free), 93 monomers, 10604.98 Da Detail

GSSHHHHHHS SGLVPRGSHM KKRAELELYE MLTEREMEIL LLIAKGYSNQ EIASASHITI KTVKTHVSNI LSKLEVQDRT QAVIYAFQHN LIQ

Formula weight

10604.98 Da

Source organism

Staphylococcus aureus

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 71.0 %, Completeness: 52.3 %, Completeness (bb): 62.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	52.3 % (573 of 1096)	48.4 % (275 of 568)	56.5 % (242 of 428)	56.0 % (56 of 100)
Backbone	62.4 % (347 of 556)	63.0 % (119 of 189)	62.5 % (172 of 275)	60.9 % (56 of 92)
Sidechain	45.0 % (283 of 629)	41.2 % (156 of 379)	52.5 % (127 of 242)	0.0 % (0 of 8)
Aromatic	13.5 % (10 of 74)	18.9 % (7 of 37)	8.1 % (3 of 37)
Methyl	86.0 % (98 of 114)	86.0 % (49 of 57)	86.0 % (49 of 57)

1. VraR

GSSHHHHHHS SGLVPRGSHM KKRAELELYE MLTEREMEIL LLIAKGYSNQ EIASASHITI KTVKTHVSNI LSKLEVQDRT QAVIYAFQHN LIQ

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308.15 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	VraR	[U-98% 15N]		0.3 mM
2	NaCl			750 mM
3	H2O			90 %
4	D2O			10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308.15 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
5	VraR	[U-98% 13C; U-98% 15N]		0.3 mM
6	NaCl			750 mM
7	H2O			90 %
8	D2O			10 %

LACS Plot; CA

Referencing offset: -0.39 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.39 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.12 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: -0.41 ppm, Outliers: 2 Detail

Release date

2015-07-22

Citation

The NMR structure of the Staphylococcus aureus response regulator VraR DNA binding domain reveals a dynamic relationship between it and its associated receiver domain
Donaldson, L.W.
Biochemistry (2008), 47, 3379-3388, PubMed 18293926 , DOI 10.1021/bi701844q , Abstract

Related entities 1. VraR, : 65 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian NMRS - 600 MHz with Gen3 salt tolerant cold probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308.15 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	VraR	[U-98% 15N]		0.3 mM
2	NaCl			750 mM
3	H2O			90 %
4	D2O			10 %

2 2D 1H-13C HSQC

Instrument

Varian NMRS - 600 MHz with Gen3 salt tolerant cold probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308.15 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	VraR	[U-98% 15N]		0.3 mM
2	NaCl			750 mM
3	H2O			90 %
4	D2O			10 %

3 3D CBCA(CO)NH

Instrument

Varian NMRS - 600 MHz with Gen3 salt tolerant cold probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308.15 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	VraR	[U-98% 15N]		0.3 mM
2	NaCl			750 mM
3	H2O			90 %
4	D2O			10 %

4 3D C(CO)NH

Instrument

Varian NMRS - 600 MHz with Gen3 salt tolerant cold probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308.15 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	VraR	[U-98% 15N]		0.3 mM
2	NaCl			750 mM
3	H2O			90 %
4	D2O			10 %

5 3D HNCACB

Instrument

Varian NMRS - 600 MHz with Gen3 salt tolerant cold probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308.15 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	VraR	[U-98% 15N]		0.3 mM
2	NaCl			750 mM
3	H2O			90 %
4	D2O			10 %

6 3D H(CCO)NH

Instrument

Varian NMRS - 600 MHz with Gen3 salt tolerant cold probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308.15 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	VraR	[U-98% 15N]		0.3 mM
2	NaCl			750 mM
3	H2O			90 %
4	D2O			10 %

7 3D HCCH-TOCSY

Instrument

Varian NMRS - 600 MHz with Gen3 salt tolerant cold probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308.15 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	VraR	[U-98% 15N]		0.3 mM
2	NaCl			750 mM
3	H2O			90 %
4	D2O			10 %

8 3D 1H-15N NOESY

Instrument

Varian NMRS - 600 MHz with Gen3 salt tolerant cold probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308.15 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	VraR	[U-98% 15N]		0.3 mM
2	NaCl			750 mM
3	H2O			90 %
4	D2O			10 %

9 3D 1H-13C NOESY

Instrument

Varian NMRS - 600 MHz with Gen3 salt tolerant cold probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308.15 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	VraR	[U-98% 15N]		0.3 mM
2	NaCl			750 mM
3	H2O			90 %
4	D2O			10 %

10 2D (HB)CB(CGCD)HD

Instrument

Varian NMRS - 600 MHz with Gen3 salt tolerant cold probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308.15 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	VraR	[U-98% 15N]		0.3 mM
2	NaCl			750 mM
3	H2O			90 %
4	D2O			10 %

11 2D (HB)CB(CGCDCE)HE

Instrument

Varian NMRS - 600 MHz with Gen3 salt tolerant cold probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308.15 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	VraR	[U-98% 15N]		0.3 mM
2	NaCl			750 mM
3	H2O			90 %
4	D2O			10 %

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr15378_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr15378_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assignments_vrar	Warning	660		69.9 (chain: 1, length: 93)
1	Chemical shift references	chemical_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assignments_vrar
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 93, Sequence coverage: 69.9%
- Total number of assignments
  - ¹H chemical shifts: 366
  - ¹³C chemical shifts: 239
  - ¹⁵N chemical shifts: 55
- Completeness of assignments
  - Entity_assemble_ID: 1
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Keywords dna binding domain, protein