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BMRB: 7377

2KJC

Resonance assignments of the metal sensor CzrA in the apo-, Zn2- and DNA-bound (42 kDa) states

Authors

Arunkumar, A.I., Pennella, M.A., Kong, X., David, G.P.

Assembly

CzrA

Entity

1. CzrA Chain (polymer, Thiol state: not present), 106 monomers, 11972.55 × 2 Da Detail

MAEQYSEINT DTLERVTEIF KALGDYNRIR IMELLSVSEA SVGHISHQLN LSQSNVSHQL KLLKSVHLVK AKRQGQSMIY SLDDIHVATM LKQAIHHANH PKESGL

2. DNA (polymer, Thiol state: not present), 28 monomers, 8664.571 Da Detail

TAACATATGA ACATATGTTC ATATGTTA

Total weight

32609.672 Da

Max. entity weight

11972.55 Da

Source organism

Staphylococcus aureus

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 79.1 %, Completeness: 44.7 %, Completeness (bb): 63.5 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	44.7 % (676 of 1512)	21.8 % (199 of 914)	75.5 % (363 of 481)	97.4 % (114 of 117)
Backbone	63.5 % (527 of 830)	27.3 % (112 of 411)	99.0 % (311 of 314)	99.0 % (104 of 105)
Sidechain	31.9 % (250 of 784)	17.3 % (87 of 503)	56.9 % (153 of 269)	83.3 % (10 of 12)
Aromatic	1.6 % (2 of 122)	2.2 % (2 of 89)	0.0 % (0 of 33)
Methyl	75.2 % (109 of 145)	66.7 % (52 of 78)	85.1 % (57 of 67)

1. CzrA Chain

MAEQYSEINT DTLERVTEIF KALGDYNRIR IMELLSVSEA SVGHISHQLN LSQSNVSHQL KLLKSVHLVK AKRQGQSMIY SLDDIHVATM LKQAIHHANH PKESGL

2. DNA

TAACATATGA ACATATGTTC ATATGTTA

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 (±2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	CzrA	[U-100% 13C; U-100% 15N; 80% 2H]	1 (±0.1) mM
2	DNA	natural abundance	1.0 ~ 1.5 mM
3	MES	[U-100% 2H]	10 (±0.5) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 (±2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
5	CzrA	[U-10% 13C]	1 (±0.1) mM
6	DNA	natural abundance	1.0 ~ 1.5 mM
7	MES	[U-100% 2H]	10 (±0.5) mM
8	sodium chloride	natural abundance	50 (±1.0) mM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 (±2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
9	CzrA	[U-2H; U-15N]; [13C]-Ile,Leu,Val-methyl	1 (±0.1) mM
10	DNA	natural abundance	1.0 ~ 1.5 mM
11	MES	[U-100% 2H]	10 (±0.5) mM
12	sodium chloride	natural abundance	50 (±1.0) mM

Sample #4

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 (±2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
13	CzrA	[U-2H; U-15N]; [13C]-Ile,Leu,Val-methyl; [U-2H]-Leu,Val-methyl	1 (±0.1) mM
14	DNA	natural abundance	1.0 ~ 1.5 mM
15	MES	[U-100% 2H]	10 (±0.5) mM
16	sodium chloride	natural abundance	50 (±1.0) mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.55 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.55 ppm, Outliers: 3 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.1 ppm, Outliers: 1 Detail

Release date

2007-08-22

Citation

Resonance assignments of the metal sensor CzrA in the apo-, Zn2- and DNA-bound (42 kDa) states
Arunkumar, A.I., Pennella, M.A., Kong, X., Giedroc, D.P.
Biomol. NMR Assign. (2007), 1, 99-101, PubMed 19636838 , DOI 10.1007/s12104-007-9027-y , Abstract

Related entities 1. CzrA Chain, : 1 : 1 : 5 : 26 entities Detail

Experiments performed 14 experiments Detail

1 2D 1H-15N TROSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 (±2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	CzrA	[U-100% 13C; U-100% 15N; 80% 2H]	1 (±0.1) mM
2	DNA	natural abundance	1.0 ~ 1.5 mM
3	MES	[U-100% 2H]	10 (±0.5) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

2 2D 1H-13C HMQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 (±2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	CzrA	[U-100% 13C; U-100% 15N; 80% 2H]	1 (±0.1) mM
2	DNA	natural abundance	1.0 ~ 1.5 mM
3	MES	[U-100% 2H]	10 (±0.5) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

3 3D TROSY-HN(COCA)CB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 (±2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	CzrA	[U-100% 13C; U-100% 15N; 80% 2H]	1 (±0.1) mM
2	DNA	natural abundance	1.0 ~ 1.5 mM
3	MES	[U-100% 2H]	10 (±0.5) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

4 3D TROSY-HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 (±2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	CzrA	[U-100% 13C; U-100% 15N; 80% 2H]	1 (±0.1) mM
2	DNA	natural abundance	1.0 ~ 1.5 mM
3	MES	[U-100% 2H]	10 (±0.5) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

5 3D TROSY-HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 (±2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	CzrA	[U-100% 13C; U-100% 15N; 80% 2H]	1 (±0.1) mM
2	DNA	natural abundance	1.0 ~ 1.5 mM
3	MES	[U-100% 2H]	10 (±0.5) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

6 3D 1H-15N NOESY-TROSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 (±2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	CzrA	[U-100% 13C; U-100% 15N; 80% 2H]	1 (±0.1) mM
2	DNA	natural abundance	1.0 ~ 1.5 mM
3	MES	[U-100% 2H]	10 (±0.5) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

7 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 (±2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	CzrA	[U-100% 13C; U-100% 15N; 80% 2H]	1 (±0.1) mM
2	DNA	natural abundance	1.0 ~ 1.5 mM
3	MES	[U-100% 2H]	10 (±0.5) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

8 4D 13C/15 NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 (±2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	CzrA	[U-100% 13C; U-100% 15N; 80% 2H]	1 (±0.1) mM
2	DNA	natural abundance	1.0 ~ 1.5 mM
3	MES	[U-100% 2H]	10 (±0.5) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

9 3D TROSY-HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 (±2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	CzrA	[U-100% 13C; U-100% 15N; 80% 2H]	1 (±0.1) mM
2	DNA	natural abundance	1.0 ~ 1.5 mM
3	MES	[U-100% 2H]	10 (±0.5) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

10 3D TROSY-HNCO (1J HN couplings)

Instrument

Varian INOVA - 600 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 (±2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	CzrA	[U-100% 13C; U-100% 15N; 80% 2H]	1 (±0.1) mM
2	DNA	natural abundance	1.0 ~ 1.5 mM
3	MES	[U-100% 2H]	10 (±0.5) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

11 3D TROSY-HNCO (1J COCA couplings)

Instrument

Varian INOVA - 600 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 (±2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	CzrA	[U-100% 13C; U-100% 15N; 80% 2H]	1 (±0.1) mM
2	DNA	natural abundance	1.0 ~ 1.5 mM
3	MES	[U-100% 2H]	10 (±0.5) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

12 3D TROSY-HNCO (1J NCA couplings)

Instrument

Varian INOVA - 600 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 (±2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	CzrA	[U-100% 13C; U-100% 15N; 80% 2H]	1 (±0.1) mM
2	DNA	natural abundance	1.0 ~ 1.5 mM
3	MES	[U-100% 2H]	10 (±0.5) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

13 2D IPAP-HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 (±2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	CzrA	[U-100% 13C; U-100% 15N; 80% 2H]	1 (±0.1) mM
2	DNA	natural abundance	1.0 ~ 1.5 mM
3	MES	[U-100% 2H]	10 (±0.5) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

14 3D HMCM[CG]CBCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 (±2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	CzrA	[U-100% 13C; U-100% 15N; 80% 2H]	1 (±0.1) mM
2	DNA	natural abundance	1.0 ~ 1.5 mM
3	MES	[U-100% 2H]	10 (±0.5) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr7377_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: bmr7377_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	745		100.0 (chain: 1, length: 106)
1	Chemical shift references	chemical_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 106, Sequence coverage: 100.0%
- Total number of assignments
  - ¹³C chemical shifts: 360
  - ¹H chemical shifts: 271
  - ¹⁵N chemical shifts: 114
- Completeness of assignments
  - Entity_assemble_ID: 1
- Peptide bond of PRO
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	481	360	74.8
¹H chemical shifts	645	173	26.8
¹⁵N chemical shifts	121	114	94.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	212	210	99.1
¹H chemical shifts	215	104	48.4
¹⁵N chemical shifts	105	104	99.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	269	150	55.8
¹H chemical shifts	430	69	16.0
¹⁵N chemical shifts	16	10	62.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	71	56	78.9
¹H chemical shifts	71	49	69.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	33	0	0.0
¹H chemical shifts	33	0	0.0

Keywords NMR

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Found 1 Document (0.836 seconds)

BMRB: 7377

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. CzrA Chain, : 1 : 1 : 5 : 26 entities Detail

Experiments performed 14 experiments Detail

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Chemical shift validation 4 contents Detail