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BMRB: 18753

2LZF

Structure of the biofilm matrix promoter AbbA from B. subtilis

Authors

Bobay, B.G., Tucker, A.T., Losick, R., Cavanagh, J.

Assembly

biofilm matrix promoter AbbA from B. subtilis

Entity

1. biofilm matrix promoter AbbA from B. subtilis (polymer, Thiol state: not present), 68 monomers, 7978.931 × 2 Da Detail

GSHMRMSLIG ERFTEEEQKL LLNILINHEY AIELLSSEIN DIETGTKNVD GTTYKKLVTL YDRFRFEN

Total weight

15957.862 Da

Max. entity weight

7978.931 Da

Source organism

Bacillus subtilis

Exptl. method

solution NMR

Refine. method

simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.1 %, Completeness: 87.7 %, Completeness (bb): 93.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.7 % (720 of 821)	86.2 % (368 of 427)	88.1 % (282 of 320)	94.6 % (70 of 74)
Backbone	93.6 % (382 of 408)	94.3 % (132 of 140)	93.0 % (186 of 200)	94.1 % (64 of 68)
Sidechain	83.6 % (399 of 477)	82.2 % (236 of 287)	85.3 % (157 of 184)	100.0 % (6 of 6)
Aromatic	35.5 % (22 of 62)	35.5 % (11 of 31)	35.5 % (11 of 31)
Methyl	100.0 % (82 of 82)	100.0 % (41 of 41)	100.0 % (41 of 41)

1. entity

GSHMRMSLIG ERFTEEEQKL LLNILINHEY AIELLSSEIN DIETGTKNVD GTTYKKLVTL YDRFRFEN

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	DTT	natural abundance	1 mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	200 mM
5	EDTA	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
9	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
10	DTT	natural abundance	1 mM
11	TRIS	natural abundance	20 mM
12	sodium chloride	natural abundance	200 mM
13	EDTA	natural abundance	1 mM
14	sodium azide	natural abundance	0.02 %
15	D2O	natural abundance	100 %

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: -0.54 ppm, Outliers: 1 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: -0.54 ppm, Outliers: 1 Detail

LACS Plot; HA

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: -0.02 ppm, Outliers: 1 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: -0.52 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2013-09-09

Citation

Structure of the biofilm matrix promoter AbbA from B. subtilis
Tucker, A.T., Bobay, B.G., Banse, A.V., Olson, A.L., Thompson, R.J., Varney, K.M., Losick, R., Cavanagh, J.
Not known

Related entities 1. biofilm matrix promoter AbbA from B. subtilis, : 1 : 1 : 1 entities Detail

Interaction partners 1. biofilm matrix promoter AbbA from B. subtilis, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 19 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 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	DTT	natural abundance	1 mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	200 mM
5	EDTA	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %
8	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 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	DTT	natural abundance	1 mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	200 mM
5	EDTA	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	DTT	natural abundance	1 mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	200 mM
5	EDTA	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

4 3D C(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	DTT	natural abundance	1 mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	200 mM
5	EDTA	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %
8	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 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	DTT	natural abundance	1 mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	200 mM
5	EDTA	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

6 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	DTT	natural abundance	1 mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	200 mM
5	EDTA	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

7 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	DTT	natural abundance	1 mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	200 mM
5	EDTA	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	DTT	natural abundance	1 mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	200 mM
5	EDTA	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

9 3D HN(CO)CA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	DTT	natural abundance	1 mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	200 mM
5	EDTA	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

10 3D H(CCO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	DTT	natural abundance	1 mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	200 mM
5	EDTA	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

11 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
9	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
10	DTT	natural abundance	1 mM
11	TRIS	natural abundance	20 mM
12	sodium chloride	natural abundance	200 mM
13	EDTA	natural abundance	1 mM
14	sodium azide	natural abundance	0.02 %
15	D2O	natural abundance	100 %

12 3D HNHA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	DTT	natural abundance	1 mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	200 mM
5	EDTA	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

13 3D 1H-15N TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	DTT	natural abundance	1 mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	200 mM
5	EDTA	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

14 3D HN(CA)CO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	DTT	natural abundance	1 mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	200 mM
5	EDTA	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

15 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	DTT	natural abundance	1 mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	200 mM
5	EDTA	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

16 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
9	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
10	DTT	natural abundance	1 mM
11	TRIS	natural abundance	20 mM
12	sodium chloride	natural abundance	200 mM
13	EDTA	natural abundance	1 mM
14	sodium azide	natural abundance	0.02 %
15	D2O	natural abundance	100 %

17 3D 13C-12C isotope filtered NOESY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
9	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
10	DTT	natural abundance	1 mM
11	TRIS	natural abundance	20 mM
12	sodium chloride	natural abundance	200 mM
13	EDTA	natural abundance	1 mM
14	sodium azide	natural abundance	0.02 %
15	D2O	natural abundance	100 %

18 2D 1H-15N HSQC RDC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	DTT	natural abundance	1 mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	200 mM
5	EDTA	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

19 2D 1H-15N HSQC RDC

Instrument

Bruker Avance - 700 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 20mM Tris (pH 6.5), 200mM NaCl, 1mM EDTA, 1mM DTT, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	DTT	natural abundance	1 mM
3	TRIS	natural abundance	20 mM
4	sodium chloride	natural abundance	200 mM
5	EDTA	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, RDC restraints	combined_18753_2lzf.nef
Input source #2: Coordindates	2lzf.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--------
GSHMRMSLIGERFTEEEQKLLLNILINHEYAIELLSSEINDIETGTKNVDGTTYKKLVTLYDRFRFEN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMRMSLIGERFTEEEQKLLLNILINHEYAIELLSSEINDIETGTKNVDGTTYKKLVTLYDRFRFEN

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

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	68	0	0	100.0
B	B	68	0	0	100.0

Content subtype: combined_18753_2lzf.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	703		95.6 (chain: A, length: 68)
1	RDC restraints	DYANA/DIANA_dipolar_coupling_5	OK	37 (37)	.	54.4 (chain: A, length: 68)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 68, Sequence coverage: 95.6%
- Total number of assignments
  - ¹H chemical shifts: 361
  - ¹³C chemical shifts: 274
  - ¹⁵N chemical shifts: 68
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	427	361	84.5
¹³C chemical shifts	320	274	85.6
¹⁵N chemical shifts	78	68	87.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	140	129	92.1
¹³C chemical shifts	136	123	90.4
¹⁵N chemical shifts	68	62	91.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	287	232	80.8
¹³C chemical shifts	184	151	82.1
¹⁵N chemical shifts	10	6	60.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	43	41	95.3
¹³C chemical shifts	43	37	86.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	11	35.5
¹³C chemical shifts	31	11	35.5

RDC restraints

Saveframe: DYANA/DIANA_dipolar_coupling_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 68, Sequence coverage: 54.4%
- Total number of restraints: 37
- Potential type of restraints: undefined (37)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords AbrB, Biofilm, DNA-mimic

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Found 1 Document (0.738 seconds)

BMRB: 18753

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. biofilm matrix promoter AbbA from B. subtilis, : 1 : 1 : 1 entities Detail

Interaction partners 1. biofilm matrix promoter AbbA from B. subtilis, : 1 interactors Detail

Experiments performed 19 experiments Detail

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NMR combined restraints 3 contents Detail