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BMRB: 17534

2LVL

NMR resonance assignment of the autoimmunity protein SpaI from Bacillus subtilis ATCC 6633

Authors

Christ, N.A., Duchardt-Ferner, E., Duesterhus, S., Koetter, P., Entian, K., Woehnert, J.

Assembly

SpaI monomer

Entity

1. SpaI monomer (polymer, Thiol state: not present), 128 monomers, 14947.23 Da Detail

GSTMHFTDDN ENDTSETMES LIDKGKLDQV VYDDQLYHLK EKVDEDKKGK VIGAIGQTFF VDGDGKRWSE EELKEPYISN NPDEIREKKP LRYGKVYSTN EDSDAKDEII VEFNREYYRA VLIKNEKE

Formula weight

14947.23 Da

Source organism

Bacillus subtilis

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 96.3 %, Completeness (bb): 97.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.3 % (1467 of 1523)	96.3 % (772 of 802)	95.9 % (561 of 585)	98.5 % (134 of 136)
Backbone	97.4 % (742 of 762)	96.6 % (252 of 261)	97.6 % (367 of 376)	98.4 % (123 of 125)
Sidechain	95.8 % (844 of 881)	96.1 % (520 of 541)	95.1 % (313 of 329)	100.0 % (11 of 11)
Aromatic	81.0 % (94 of 116)	82.8 % (48 of 58)	78.9 % (45 of 57)	100.0 % (1 of 1)
Methyl	98.2 % (108 of 110)	96.4 % (53 of 55)	100.0 % (55 of 55)

1. SpaI

GSTMHFTDDN ENDTSETMES LIDKGKLDQV VYDDQLYHLK EKVDEDKKGK VIGAIGQTFF VDGDGKRWSE EELKEPYISN NPDEIREKKP LRYGKVYSTN EDSDAKDEII VEFNREYYRA VLIKNEKE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	100 mM
3	DSS	natural abundance	10 uM
4	SpaI	[U-15N]	300.0 ~ 400.0 uM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	DSS	natural abundance	10 uM
10	SpaI	[U-13C; U-15N; U-2H]	420 uM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
13	sodium phosphate	natural abundance	50 mM
14	sodium chloride	natural abundance	100 mM
15	DSS	natural abundance	10 uM
16	SpaI	[U-13C; U-15N]	300.0 ~ 400.0 uM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

Sample #4

Solvent system 90% D2O/10% H2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
19	sodium phosphate	natural abundance	50 mM
20	sodium chloride	natural abundance	100 mM
21	DSS	natural abundance	10 uM
22	SpaI	[U-13C; U-15N]	300 uM
23	H2O	natural abundance	90 %
24	D2O	natural abundance	10 %

LACS Plot; CA

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

Referencing offset: -0.16 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.16 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.03 ppm, Outliers: 5 Detail

LACS Plot; CO

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

Referencing offset: 0.34 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LVL, Strand ID: A Detail

Release date

2012-05-09

Citation

NMR resonance assignment of the autoimmunity protein SpaI from Bacillus subtilis ATCC 6633
Christ, N., Duchardt-Ferner, E., Dusterhus, S., Kotter, P., Entian, K., Wohnert, J.
Biomol. NMR Assign. (2012), 6, 9-13, PubMed 21643970 , DOI 10.1007/s12104-011-9314-5 , Abstract

Related entities 1. SpaI monomer, : 1 : 1 entities Detail

Experiments performed 18 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	100 mM
3	DSS	natural abundance	10 uM
4	SpaI	[U-15N]	300.0 ~ 400.0 uM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% D2O/10% H2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
19	sodium phosphate	natural abundance	50 mM
20	sodium chloride	natural abundance	100 mM
21	DSS	natural abundance	10 uM
22	SpaI	[U-13C; U-15N]	300 uM
23	H2O	natural abundance	90 %
24	D2O	natural abundance	10 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
13	sodium phosphate	natural abundance	50 mM
14	sodium chloride	natural abundance	100 mM
15	DSS	natural abundance	10 uM
16	SpaI	[U-13C; U-15N]	300.0 ~ 400.0 uM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
13	sodium phosphate	natural abundance	50 mM
14	sodium chloride	natural abundance	100 mM
15	DSS	natural abundance	10 uM
16	SpaI	[U-13C; U-15N]	300.0 ~ 400.0 uM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

5 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	DSS	natural abundance	10 uM
10	SpaI	[U-13C; U-15N; U-2H]	420 uM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

6 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	DSS	natural abundance	10 uM
10	SpaI	[U-13C; U-15N; U-2H]	420 uM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

7 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	DSS	natural abundance	10 uM
10	SpaI	[U-13C; U-15N; U-2H]	420 uM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
13	sodium phosphate	natural abundance	50 mM
14	sodium chloride	natural abundance	100 mM
15	DSS	natural abundance	10 uM
16	SpaI	[U-13C; U-15N]	300.0 ~ 400.0 uM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

9 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
13	sodium phosphate	natural abundance	50 mM
14	sodium chloride	natural abundance	100 mM
15	DSS	natural abundance	10 uM
16	SpaI	[U-13C; U-15N]	300.0 ~ 400.0 uM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

10 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
13	sodium phosphate	natural abundance	50 mM
14	sodium chloride	natural abundance	100 mM
15	DSS	natural abundance	10 uM
16	SpaI	[U-13C; U-15N]	300.0 ~ 400.0 uM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

11 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% D2O/10% H2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
19	sodium phosphate	natural abundance	50 mM
20	sodium chloride	natural abundance	100 mM
21	DSS	natural abundance	10 uM
22	SpaI	[U-13C; U-15N]	300 uM
23	H2O	natural abundance	90 %
24	D2O	natural abundance	10 %

12 3D HCCH-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% D2O/10% H2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
19	sodium phosphate	natural abundance	50 mM
20	sodium chloride	natural abundance	100 mM
21	DSS	natural abundance	10 uM
22	SpaI	[U-13C; U-15N]	300 uM
23	H2O	natural abundance	90 %
24	D2O	natural abundance	10 %

13 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	100 mM
3	DSS	natural abundance	10 uM
4	SpaI	[U-15N]	300.0 ~ 400.0 uM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

14 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	100 mM
3	DSS	natural abundance	10 uM
4	SpaI	[U-15N]	300.0 ~ 400.0 uM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

15 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
13	sodium phosphate	natural abundance	50 mM
14	sodium chloride	natural abundance	100 mM
15	DSS	natural abundance	10 uM
16	SpaI	[U-13C; U-15N]	300.0 ~ 400.0 uM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

16 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% D2O/10% H2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
19	sodium phosphate	natural abundance	50 mM
20	sodium chloride	natural abundance	100 mM
21	DSS	natural abundance	10 uM
22	SpaI	[U-13C; U-15N]	300 uM
23	H2O	natural abundance	90 %
24	D2O	natural abundance	10 %

17 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
13	sodium phosphate	natural abundance	50 mM
14	sodium chloride	natural abundance	100 mM
15	DSS	natural abundance	10 uM
16	SpaI	[U-13C; U-15N]	300.0 ~ 400.0 uM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

18 3D HNCACO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.4

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	DSS	natural abundance	10 uM
10	SpaI	[U-13C; U-15N; U-2H]	420 uM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_17534_2lvl.nef
Input source #2: Coordindates	2lvl.cif
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

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
GSTMHFTDDNENDTSETMESLIDKGKLDQVVYDDQLYHLKEKVDEDKKGKVIGAIGQTFFVDGDGKRWSEEELKEPYISNNPDEIREKKPLRYGKVYSTN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSTMHFTDDNENDTSETMESLIDKGKLDQVVYDDQLYHLKEKVDEDKKGKVIGAIGQTFFVDGDGKRWSEEELKEPYISNNPDEIREKKPLRYGKVYSTN

-------110-------120--------
EDSDAKDEIIVEFNREYYRAVLIKNEKE
||||||||||||||||||||||||||||
EDSDAKDEIIVEFNREYYRAVLIKNEKE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	128	0	0	100.0

Content subtype: combined_17534_2lvl.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1484		99.2 (chain: A, length: 128)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	4376 (1)	noe	98.4 (chain: A, length: 128)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	36 (1)	hbond	20.3 (chain: A, length: 128)
3	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	72 (1)	hbond	20.3 (chain: A, length: 128)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	271 (271)	.	100.0 (chain: A, length: 128)
1	RDC restraints	DYANA/DIANA_dipolar_coupling_5	OK	60 (60)	.	46.9 (chain: A, length: 128)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 99.2%
- Total number of assignments
  - ¹H chemical shifts: 783
  - ¹³C chemical shifts: 564
  - ¹⁵N chemical shifts: 137
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Tautomeric state of HIS
- 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: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	802	783	97.6
¹³C chemical shifts	585	564	96.4
¹⁵N chemical shifts	141	137	97.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	261	257	98.5
¹³C chemical shifts	256	250	97.7
¹⁵N chemical shifts	125	123	98.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	541	526	97.2
¹³C chemical shifts	329	314	95.4
¹⁵N chemical shifts	16	14	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	57	55	96.5
¹³C chemical shifts	57	55	96.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	47	81.0
¹³C chemical shifts	57	44	77.2
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 98.4%
- Total number of restraints: 4343
- Weight of restraints: 1.0 (4343)
- Potential type of restraints: upper-bound-parabolic (4343)
- Range of distance target values: 2.61, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 20.3%
  - Total number of restraints: 36
  - Weight of restraints: 1.0 (36)
  - Potential type of restraints: upper-bound-parabolic (36)
  - Range of distance target values: 2.2, 3.2 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_6
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 20.3%
    - Total number of restraints: 72
    - Weight of restraints: 1.0 (72)
    - Potential type of restraints: upper-bound-parabolic (72)
    - Range of distance target values: 1.8, 3.2 (Å)
    - Histogram of distance target values
    - Histogram of discrepancy in distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 100.0%
- Total number of restraints: 271
- Total number of restraints per polymer type: 271
- Weight of restraints: 1.0 (271)
- Potential type of restraints: square-well-parabolic (271)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: DYANA/DIANA_dipolar_coupling_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 46.9%
- Total number of restraints: 60
- Potential type of restraints: undefined (60)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

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Found 1 Document (0.7 seconds)

BMRB: 17534

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. SpaI monomer, : 1 : 1 entities Detail

Experiments performed 18 experiments Detail

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NMR combined restraints 7 contents Detail