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BMRB: 16961

2KYI

Solution NMR structure of Dsy0195(21-82) protein from Desulfitobacterium Hafniense. Northeast Structural Genomics Consortium Target DhR8C.

Authors

Yang, Y., Ramelot, T.A., Cort, J.R., Wang, H., Ciccosanti, C., Foote, E.L., Jiang, M., Janjua, H., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Kennedy, M.A.

Assembly

Dsy0195(21-82) protein

Entity

1. Dsy0195(21-82) protein (polymer, Thiol state: not present), 71 monomers, 7988.092 Da Detail

MDNRQFLSLT GVSKVQSFDP KEILLETIQG VLSIKGEKLG IKHLDLKAGQ VEVEGLIDAL VYPLEHHHHH H

Formula weight

7988.092 Da

Source organism

Desulfitobacterium hafniense

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 95.8 %, Completeness: 91.1 %, Completeness (bb): 93.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.1 % (770 of 845)	92.5 % (405 of 438)	88.3 % (294 of 333)	95.9 % (71 of 74)
Backbone	93.4 % (394 of 422)	95.9 % (140 of 146)	90.8 % (188 of 207)	95.7 % (66 of 69)
Sidechain	89.5 % (437 of 488)	90.8 % (265 of 292)	87.4 % (167 of 191)	100.0 % (5 of 5)
Aromatic	50.0 % (28 of 56)	50.0 % (14 of 28)	50.0 % (14 of 28)
Methyl	95.8 % (92 of 96)	95.8 % (46 of 48)	95.8 % (46 of 48)

1. Dsy0195(21-82) protein

MDNRQFLSLT GVSKVQSFDP KEILLETIQG VLSIKGEKLG IKHLDLKAGQ VEVEGLIDAL VYPLEHHHHH H

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	ammonium acetate	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	200 (±10.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
7	Dsy0195(21-82) protein	[U-5% 13C; U-100% 15N]	1 (±0.09) mM
8	ammonium acetate	natural abundance	20 (±1.0) mM
9	sodium chloride	natural abundance	200 (±10.0) mM
10	calcium chloride	natural abundance	5 (±0.2) mM
11	DTT	natural abundance	10 (±0.5) mM
12	sodium azide	natural abundance	0.02 (±0.001) %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
13	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
14	ammonium acetate	natural abundance	20 (±1.0) mM
15	sodium chloride	natural abundance	200 (±10.0) mM
16	calcium chloride	natural abundance	5 (±0.2) mM
17	DTT	natural abundance	10 (±0.5) mM
18	sodium azide	natural abundance	0.02 (±0.001) %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1), Details mixture of [U-100% 13C; U-100% 15N]DhR8C and natural abundance DhR8C at a concentration ratio 1:1(mM:mM).

#	Name	Isotope labeling	Concentration
19	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
20	Dsy0195(21-82) protein	natural abundance	1.0 (±0.1) mM
21	ammonium acetate	natural abundance	20 (±1.0) mM
22	sodium chloride	natural abundance	200 (±10.0) mM
23	calcium chloride	natural abundance	5 (±0.2) mM
24	DTT	natural abundance	10 (±0.5) mM
25	sodium azide	natural abundance	0.02 (±0.001) %

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: -0.18 ppm, Outliers: 2 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: -0.18 ppm, Outliers: 2 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: -0.16 ppm, Outliers: 1 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: 0.77 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2012-08-01

Citation

Solution NMR structure of Dsy0195 homodimer from Desulfitobacterium hafniense: first structure representative of the YabP domain family of proteins involved in spore coat assembly
Yang, Y., Ramelot, T.A., Cort, J.R., Wang, H., Ciccosanti, C., Foote, E.L., Jiang, M., Janjua, H., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Kennedy, M.A.
J. Struct. Funct. Genomics (2011), 12, 175-179, PubMed 21904870 , DOI 10.1007/s10969-011-9117-z , Abstract

Related entities 1. Dsy0195(21-82) protein, : 1 : 2 : 5 entities Detail

Experiments performed 20 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	ammonium acetate	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	200 (±10.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

2 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	ammonium acetate	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	200 (±10.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

3 2D 1H-13C HSQC_CT

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
7	Dsy0195(21-82) protein	[U-5% 13C; U-100% 15N]	1 (±0.09) mM
8	ammonium acetate	natural abundance	20 (±1.0) mM
9	sodium chloride	natural abundance	200 (±10.0) mM
10	calcium chloride	natural abundance	5 (±0.2) mM
11	DTT	natural abundance	10 (±0.5) mM
12	sodium azide	natural abundance	0.02 (±0.001) %

4 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	ammonium acetate	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	200 (±10.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

5 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	ammonium acetate	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	200 (±10.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

6 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	ammonium acetate	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	200 (±10.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

7 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	ammonium acetate	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	200 (±10.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

8 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	ammonium acetate	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	200 (±10.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

9 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	ammonium acetate	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	200 (±10.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

10 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	ammonium acetate	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	200 (±10.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

11 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	ammonium acetate	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	200 (±10.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

12 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	ammonium acetate	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	200 (±10.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

13 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	ammonium acetate	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	200 (±10.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

14 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	ammonium acetate	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	200 (±10.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

15 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	ammonium acetate	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	200 (±10.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

16 3D (H)CCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
13	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
14	ammonium acetate	natural abundance	20 (±1.0) mM
15	sodium chloride	natural abundance	200 (±10.0) mM
16	calcium chloride	natural abundance	5 (±0.2) mM
17	DTT	natural abundance	10 (±0.5) mM
18	sodium azide	natural abundance	0.02 (±0.001) %

17 4D CC NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
13	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
14	ammonium acetate	natural abundance	20 (±1.0) mM
15	sodium chloride	natural abundance	200 (±10.0) mM
16	calcium chloride	natural abundance	5 (±0.2) mM
17	DTT	natural abundance	10 (±0.5) mM
18	sodium azide	natural abundance	0.02 (±0.001) %

18 3D edited/filtered Cnoesy

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1), Details mixture of [U-100% 13C; U-100% 15N]DhR8C and natural abundance DhR8C at a concentration ratio 1:1(mM:mM).

#	Name	Isotope labeling	Concentration
19	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
20	Dsy0195(21-82) protein	natural abundance	1.0 (±0.1) mM
21	ammonium acetate	natural abundance	20 (±1.0) mM
22	sodium chloride	natural abundance	200 (±10.0) mM
23	calcium chloride	natural abundance	5 (±0.2) mM
24	DTT	natural abundance	10 (±0.5) mM
25	sodium azide	natural abundance	0.02 (±0.001) %

19 2D 1H-15N HSQC_Histidine

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	ammonium acetate	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	200 (±10.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

20 2D 1H-15N HSQC_swN150ppm

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 4.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Dsy0195(21-82) protein	[U-100% 13C; U-100% 15N]	1.0 (±0.1) mM
2	ammonium acetate	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	200 (±10.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

nullKeywords Desulfitobacterium Hafniense, Dsy0195 gene, Solution NMR, YabP family

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Found 1 Document (0.97 seconds)

BMRB: 16961

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Dsy0195(21-82) protein, : 1 : 2 : 5 entities Detail

Experiments performed 20 experiments Detail

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