BMRBj - BMREntryMaster

Found 1 Document (0.536 seconds)

BMRB: 30192

5TMX

Solution Structure of SinI, antagonist to the master biofilm-regulator SinR in Bacillus subtilis

Authors

Draughn, G.L., Bobay, B.G., Stowe, S.D., Thompson, R.J., Cavanagh, J.

Assembly

Protein SinI

Entity

1. Protein SinI (polymer, Thiol state: not present), 63 monomers, 7172.051 × 2 Da Detail

GSHMASMKNA KQEHFELDQE WVELMVEAKE ANISPEEIRK YLLLNKKSAH PGPAARSHTV NPF

Total weight

14344.102 Da

Max. entity weight

7172.051 Da

Source organism

Bacillus subtilis subsp. subtilis str. 168

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.7 %, Completeness: 85.8 %, Completeness (bb): 89.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.8 % (642 of 748)	86.0 % (339 of 394)	87.5 % (252 of 288)	77.3 % (51 of 66)
Backbone	89.2 % (330 of 370)	87.1 % (108 of 124)	91.4 % (171 of 187)	86.4 % (51 of 59)
Sidechain	84.3 % (370 of 439)	85.6 % (231 of 270)	85.8 % (139 of 162)	0.0 % (0 of 7)
Aromatic	46.4 % (26 of 56)	46.4 % (13 of 28)	48.1 % (13 of 27)	0.0 % (0 of 1)
Methyl	89.3 % (50 of 56)	89.3 % (25 of 28)	89.3 % (25 of 28)

1. Protein SinI

GSHMASMKNA KQEHFELDQE WVELMVEAKE ANISPEEIRK YLLLNKKSAH PGPAARSHTV NPF

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6, Details 1 mM [U-15N] SinI, 20 mM MES, 200 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	20 mM
2	NaCl	natural abundance	200 mM
3	SinI	[U-15N]	1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6, Details 1 mM [U-13C; U-15N] SinI, 20 mM MES, 200 mM NaCl, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	MES	natural abundance	20 mM
7	NaCl	natural abundance	200 mM
8	SinI	[U-13C; U-15N]	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6, Details 1 mM [U-13C; U-15N] SinI, 20 mM MES, 200 mM NaCl, 100% D2O

#	Name	Isotope labeling	Concentration
11	MES	natural abundance	20 mM
12	NaCl	natural abundance	200 mM
13	SinI	[U-13C; U-15N]	1 mM
14	D2O	natural abundance	100 %

LACS Plot; CA

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

Referencing offset: 0.13 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.13 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.06 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: -0.15 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 5TMX, Strand ID: A, B Detail

Release date

2016-11-10

Citation

The Solution Structures and Interaction of SinR and SinI: Elucidating the Mechanism of Action of the Master Regulator Switch for Biofilm Formation in Bacillus subtilis
Milton, M.E., Draughn, G.L., Bobay, B.G., Stowe, S.D., Olson, A.L., Feldmann, E.A., Thompson, R.J., Myers, K.H., Santoro, M.T., Kearns, D.B., Cavanagh, J.
J. Mol. Biol. (2020), 432, 343-357, PubMed 31493408 , DOI 10.1016/j.jmb.2019.08.019 , Abstract

Related entities 1. Protein SinI, : 1 : 2 : 3 entities Detail

Interaction partners 1. Protein SinI, : 2 interactors Detail

More details for 2 interactors identified by 1 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6, Details 1 mM [U-15N] SinI, 20 mM MES, 200 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	20 mM
2	NaCl	natural abundance	200 mM
3	SinI	[U-15N]	1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6, Details 1 mM [U-13C; U-15N] SinI, 20 mM MES, 200 mM NaCl, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	MES	natural abundance	20 mM
7	NaCl	natural abundance	200 mM
8	SinI	[U-13C; U-15N]	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

3 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6, Details 1 mM [U-13C; U-15N] SinI, 20 mM MES, 200 mM NaCl, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	MES	natural abundance	20 mM
7	NaCl	natural abundance	200 mM
8	SinI	[U-13C; U-15N]	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

4 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6, Details 1 mM [U-13C; U-15N] SinI, 20 mM MES, 200 mM NaCl, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	MES	natural abundance	20 mM
7	NaCl	natural abundance	200 mM
8	SinI	[U-13C; U-15N]	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

5 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6, Details 1 mM [U-13C; U-15N] SinI, 20 mM MES, 200 mM NaCl, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	MES	natural abundance	20 mM
7	NaCl	natural abundance	200 mM
8	SinI	[U-13C; U-15N]	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

6 3D HNCOCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6, Details 1 mM [U-13C; U-15N] SinI, 20 mM MES, 200 mM NaCl, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	MES	natural abundance	20 mM
7	NaCl	natural abundance	200 mM
8	SinI	[U-13C; U-15N]	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

7 3D HNCACO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6, Details 1 mM [U-13C; U-15N] SinI, 20 mM MES, 200 mM NaCl, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	MES	natural abundance	20 mM
7	NaCl	natural abundance	200 mM
8	SinI	[U-13C; U-15N]	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

8 3D 1H-15N TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6, Details 1 mM [U-13C; U-15N] SinI, 20 mM MES, 200 mM NaCl, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	MES	natural abundance	20 mM
7	NaCl	natural abundance	200 mM
8	SinI	[U-13C; U-15N]	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

9 3D C(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6, Details 1 mM [U-13C; U-15N] SinI, 20 mM MES, 200 mM NaCl, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	MES	natural abundance	20 mM
7	NaCl	natural abundance	200 mM
8	SinI	[U-13C; U-15N]	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6, Details 1 mM [U-15N] SinI, 20 mM MES, 200 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	20 mM
2	NaCl	natural abundance	200 mM
3	SinI	[U-15N]	1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

11 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6, Details 1 mM [U-13C; U-15N] SinI, 20 mM MES, 200 mM NaCl, 100% D2O

#	Name	Isotope labeling	Concentration
11	MES	natural abundance	20 mM
12	NaCl	natural abundance	200 mM
13	SinI	[U-13C; U-15N]	1 mM
14	D2O	natural abundance	100 %

12 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6, Details 1 mM [U-13C; U-15N] SinI, 20 mM MES, 200 mM NaCl, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	MES	natural abundance	20 mM
7	NaCl	natural abundance	200 mM
8	SinI	[U-13C; U-15N]	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30192_5tmx.nef
Input source #2: Coordindates	5tmx.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---
GSHMASMKNAKQEHFELDQEWVELMVEAKEANISPEEIRKYLLLNKKSAHPGPAARSHTVNPF
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMASMKNAKQEHFELDQEWVELMVEAKEANISPEEIRKYLLLNKKSAHPGPAARSHTVNPF

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

--------10--------20--------30--------40--------50--------60---
GSHMASMKNAKQEHFELDQEWVELMVEAKEANISPEEIRKYLLLNKKSAHPGPAARSHTVNPF
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMASMKNAKQEHFELDQEWVELMVEAKEANISPEEIRKYLLLNKKSAHPGPAARSHTVNPF

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	63	0	0	100.0
B	B	63	0	0	100.0

Content subtype: combined_30192_5tmx.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	643		93.7 (chain: A, length: 63)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	793 (1)	noe	77.8 (chain: A, length: 63), 76.2 (chain: B, length: 63)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	84 (84)	.	39.7 (chain: A, length: 63), 39.7 (chain: B, length: 63)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 93.7%
- Total number of assignments
  - ¹H chemical shifts: 340
  - ¹³C chemical shifts: 252
  - ¹⁵N chemical shifts: 51
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	394	340	86.3
¹³C chemical shifts	288	252	87.5
¹⁵N chemical shifts	68	51	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	124	110	88.7
¹³C chemical shifts	126	113	89.7
¹⁵N chemical shifts	59	51	86.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	270	230	85.2
¹³C chemical shifts	162	139	85.8
¹⁵N chemical shifts	9	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	25	80.6
¹³C chemical shifts	31	25	80.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	13	46.4
¹³C chemical shifts	27	13	48.1
¹⁵N chemical shifts	1	0	0.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 77.8%
  - Entity_assembly_ID: B, Chain length: 63, Sequence coverage: 76.2%
- Total number of restraints: 786
- Weight of restraints: 1.0 (786)
- Potential type of restraints: upper-bound-parabolic (786)
- Range of distance target values: 2.3, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 39.7%
  - Entity_assembly_ID: B, Chain length: 63, Sequence coverage: 39.7%
- Total number of restraints: 84
- Total number of restraints per polymer type: 84
- Weight of restraints: 1.0 (84)
- Potential type of restraints: square-well-parabolic (84)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords biofilm, repressor, sporulation

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Found 1 Document (0.536 seconds)

BMRB: 30192

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Protein SinI, : 1 : 2 : 3 entities Detail

Interaction partners 1. Protein SinI, : 2 interactors Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 4 contents Detail