BMRBj - BMREntryMaster

Found 1 Document (0.787 seconds)

BMRB: 30194

5TN2

Solution Structure of the C-terminal multimerization domain of the master biofilm-regulator SinR from Bacillus subtilis

Authors

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

Assembly

HTH-type transcriptional regulator SinR

Entity

1. HTH-type transcriptional regulator SinR (polymer, Thiol state: not present), 47 monomers, 5712.256 × 4 Da Detail

GSHMEYDGQL DSEWEKLVRD AMTSGVSKKQ FREFLDYQKW RKSQKEE

Total weight

22849.023 Da

Max. entity weight

5712.256 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: 100.0 %, Completeness: 93.8 %, Completeness (bb): 97.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.8 % (549 of 585)	92.0 % (287 of 312)	95.5 % (210 of 220)	98.1 % (52 of 53)
Backbone	97.5 % (275 of 282)	95.9 % (93 of 97)	98.6 % (136 of 138)	97.9 % (46 of 47)
Sidechain	91.6 % (318 of 347)	90.2 % (194 of 215)	93.7 % (118 of 126)	100.0 % (6 of 6)
Aromatic	81.3 % (52 of 64)	84.4 % (27 of 32)	76.7 % (23 of 30)	100.0 % (2 of 2)
Methyl	91.7 % (22 of 24)	83.3 % (10 of 12)	100.0 % (12 of 12)

1. HTH-type transcriptional regulator SinR

GSHMEYDGQL DSEWEKLVRD AMTSGVSKKQ FREFLDYQKW RKSQKEE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6, Details 1 mM [U-15N] SinRC, 20 mM MES, 200 mM sodium chloride, 0.02 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	20 mM
2	SinRC	[U-15N]	1 mM
3	sodium azide	natural abundance	0.02 %
4	sodium chloride	natural abundance	200 mM
5	H2O	natural abundance	90 %
6	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] SinRC, 20 mM MES, 200 mM sodium chloride, 0.02 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	MES	natural abundance	20 mM
8	SinRC	[U-13C; U-15N]	1 mM
9	sodium azide	natural abundance	0.02 %
10	sodium chloride	natural abundance	200 mM
11	H2O	natural abundance	90 %
12	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] SinRC, 20 mM MES, 200 mM sodium chloride, 0.02 % sodium azide, 100% D2O

#	Name	Isotope labeling	Concentration
13	MES	natural abundance	20 mM
14	SinRC	[U-13C; U-15N]	1 mM
15	sodium azide	natural abundance	0.02 %
16	sodium chloride	natural abundance	200 mM
17	D2O	natural abundance	100 %

Protein Blocks Logo

Calculated from 10 models in PDB: 5TN2, Strand ID: A, B, C, D Detail

Release date

2016-11-27

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. HTH-type transcriptional regulator SinR, : 1 : 3 : 7 entities Detail

Interaction partners 1. HTH-type transcriptional regulator SinR, : 3 interactors Detail

More details for 3 interactors identified by 2 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] SinRC, 20 mM MES, 200 mM sodium chloride, 0.02 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	20 mM
2	SinRC	[U-15N]	1 mM
3	sodium azide	natural abundance	0.02 %
4	sodium chloride	natural abundance	200 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

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] SinRC, 20 mM MES, 200 mM sodium chloride, 0.02 % sodium azide, 100% D2O

#	Name	Isotope labeling	Concentration
13	MES	natural abundance	20 mM
14	SinRC	[U-13C; U-15N]	1 mM
15	sodium azide	natural abundance	0.02 %
16	sodium chloride	natural abundance	200 mM
17	D2O	natural abundance	100 %

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] SinRC, 20 mM MES, 200 mM sodium chloride, 0.02 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	MES	natural abundance	20 mM
8	SinRC	[U-13C; U-15N]	1 mM
9	sodium azide	natural abundance	0.02 %
10	sodium chloride	natural abundance	200 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

4 3D HN(CO)CA

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
7	MES	natural abundance	20 mM
8	SinRC	[U-13C; U-15N]	1 mM
9	sodium azide	natural abundance	0.02 %
10	sodium chloride	natural abundance	200 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

5 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
7	MES	natural abundance	20 mM
8	SinRC	[U-13C; U-15N]	1 mM
9	sodium azide	natural abundance	0.02 %
10	sodium chloride	natural abundance	200 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

6 3D HN(CA)CO

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
7	MES	natural abundance	20 mM
8	SinRC	[U-13C; U-15N]	1 mM
9	sodium azide	natural abundance	0.02 %
10	sodium chloride	natural abundance	200 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

7 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
7	MES	natural abundance	20 mM
8	SinRC	[U-13C; U-15N]	1 mM
9	sodium azide	natural abundance	0.02 %
10	sodium chloride	natural abundance	200 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

8 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
7	MES	natural abundance	20 mM
8	SinRC	[U-13C; U-15N]	1 mM
9	sodium azide	natural abundance	0.02 %
10	sodium chloride	natural abundance	200 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

9 3D 1H-15N TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	20 mM
2	SinRC	[U-15N]	1 mM
3	sodium azide	natural abundance	0.02 %
4	sodium chloride	natural abundance	200 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

10 3D C(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
7	MES	natural abundance	20 mM
8	SinRC	[U-13C; U-15N]	1 mM
9	sodium azide	natural abundance	0.02 %
10	sodium chloride	natural abundance	200 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	20 mM
2	SinRC	[U-15N]	1 mM
3	sodium azide	natural abundance	0.02 %
4	sodium chloride	natural abundance	200 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

12 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
13	MES	natural abundance	20 mM
14	SinRC	[U-13C; U-15N]	1 mM
15	sodium azide	natural abundance	0.02 %
16	sodium chloride	natural abundance	200 mM
17	D2O	natural abundance	100 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30194_5tn2.nef
Input source #2: Coordindates	5tn2.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-------
GSHMEYDGQLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQKEE
|||||||||||||||||||||||||||||||||||||||||||||||
GSHMEYDGQLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQKEE

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

--------10--------20--------30--------40-------
GSHMEYDGQLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQKEE
|||||||||||||||||||||||||||||||||||||||||||||||
GSHMEYDGQLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQKEE

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

--------10--------20--------30--------40-------
GSHMEYDGQLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQKEE
|||||||||||||||||||||||||||||||||||||||||||||||
GSHMEYDGQLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQKEE

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

--------10--------20--------30--------40-------
GSHMEYDGQLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQKEE
|||||||||||||||||||||||||||||||||||||||||||||||
GSHMEYDGQLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQKEE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	47	100.0
B	B	47	100.0
C	C	47	100.0
D	D	47	100.0

Content subtype: combined_30194_5tn2.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	552		97.9 (chain: A, length: 47)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1896 (1)	noe	95.7 (chain: A, length: 47), 12.8 (chain: B, length: 47)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	50 (50)	.	66.0 (chain: A, length: 47)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 97.9%
- Total number of assignments
  - ¹³C chemical shifts: 210
  - ¹H chemical shifts: 288
  - ¹⁵N chemical shifts: 54
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
9	GLN	CD	180.053
30	GLN	CD	179.933
38	GLN	CD	178.101
44	GLN	CD	180.053

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	220	206	93.6
¹H chemical shifts	312	288	92.3
¹⁵N chemical shifts	56	54	96.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	94	91	96.8
¹H chemical shifts	97	92	94.8
¹⁵N chemical shifts	47	45	95.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	126	115	91.3
¹H chemical shifts	215	196	91.2
¹⁵N chemical shifts	9	9	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	14	14	100.0
¹H chemical shifts	14	12	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	30	23	76.7
¹H chemical shifts	32	27	84.4
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 47, Sequence coverage: 95.7%
  - Entity_assembly_ID: B, Chain length: 47, Sequence coverage: 12.8%
- Total number of restraints: 1840
- Weight of restraints: 1.0 (1840)
- Potential type of restraints: upper-bound-parabolic (1840)
- Range of distance target values: 2.0, 6.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
    None
  - Chain_ID: D
    None
- 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: 47, Sequence coverage: 66.0%
- Total number of restraints: 50
- Total number of restraints per polymer type: 50
- Weight of restraints: 1.0 (50)
- Potential type of restraints: square-well-parabolic (50)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords biofilm formation, multimerization domain

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.787 seconds)

BMRB: 30194

Sample #1

Sample #2

Sample #3

Related entities 1. HTH-type transcriptional regulator SinR, : 1 : 3 : 7 entities Detail

Interaction partners 1. HTH-type transcriptional regulator SinR, : 3 interactors Detail

Experiments performed 12 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail