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BMRB: 7274

2HH8

Solution NMR structure of the YdfO protein from Escherichia coli. Northeast Structural Genomics target ER251

Authors

Rossi, P., Cort, J.R., Ho, C.K., Janjua, H., Cunningham, K., Ma, L., Xiao, R., Liu, J., Baran, M., Swapna, G.V.T., Acton, T.B., Rost, B., Kennedy, M.A., Montelione, G.T.

Assembly

Hypothetical protein YdfO

Entity

1. Hypothetical protein YdfO (polymer, Thiol state: not present), 149 monomers, 18113.43 Da Detail

MEGLSMDQVV IFKQIFDKVR NDLNYQWFYS ELKRHNVSHY IYYLATENVH IVLKNDNTVL LKGLKNIVSV KFSKDRHLIE TTSNKLKSRE ITFQEYRRNL AKAGVFRWVT NIHEQKRYYY TFDNSLLFTE SIQKTTQIFP RLEHHHHHH

Formula weight

18113.43 Da

Source organism

Escherichia coli

Exptl. method

NMR

Refine. method

Noesy assignments made with iterative method using CS, 3J, Hyper (dihedral), and Dyana for simulated annealing MD. Converged structures are further refined using NIH-xplor followed by CNS in explicit water shell (Nielges) . Full lenght sequence was carried through the refinement protocol, the disordered regions and hexHIS tag are not reported. Structure based on 1885 constraints, 788 long range, 142 dihedral constraints and 114 H-bond constraints.

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.3 %, Completeness: 89.3 %, Completeness (bb): 95.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.3 % (1693 of 1896)	85.9 % (849 of 988)	92.0 % (681 of 740)	97.0 % (163 of 168)
Backbone	95.4 % (851 of 892)	95.0 % (285 of 300)	95.5 % (424 of 444)	95.9 % (142 of 148)
Sidechain	84.3 % (970 of 1150)	81.3 % (559 of 688)	88.5 % (391 of 442)	100.0 % (20 of 20)
Aromatic	72.2 % (166 of 230)	73.9 % (85 of 115)	69.9 % (79 of 113)	100.0 % (2 of 2)
Methyl	95.8 % (159 of 166)	95.2 % (79 of 83)	96.4 % (80 of 83)

1. Hypothetical protein YdfO

MEGLSMDQVV IFKQIFDKVR NDLNYQWFYS ELKRHNVSHY IYYLATENVH IVLKNDNTVL LKGLKNIVSV KFSKDRHLIE TTSNKLKSRE ITFQEYRRNL AKAGVFRWVT NIHEQKRYYY TFDNSLLFTE SIQKTTQIFP RLEHHHHHH

Show sample condition

Sample

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
2	NaN3		0.02 %
3	DTT		10 mM
4	CaCl2		5 mM
5	NaCl		100 mM
6	ammonium acetate		20 mM
7	D2O		5 %
8	H2O		95 %

LACS Plot; CA

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

Referencing offset: 0.0 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.22 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2HH8, Strand ID: A Detail

Release date

2007-01-31

Citation

NMR structure of lipoprotein YxeF from Bacillus subtilis reveals a calycin fold and distant homology with the lipocalin Blc from Escherichia coli
Rossi, P., Cort, J.R., Ho, C.K., Janjua, H., Cunningham, K., Ma, L., Xiao, R., Liu, J., Baran, M., Swapna, G.V.T., Acton, T.B., Rost, B., Kennedy, M.A., Montelione, G.T.
PLoS One (2012), 7, e37404-e37404, PubMed 22693626 , DOI 10.1371/journal.pone.0037404 , Abstract

Related entities 1. Hypothetical protein YdfO, : 1 : 2 : 8 entities Detail

Experiments performed 12 experiments Detail

1 3D 13C-separated NOESY

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
2	NaN3		0.02 %
3	DTT		10 mM
4	CaCl2		5 mM
5	NaCl		100 mM
6	ammonium acetate		20 mM
7	D2O		5 %
8	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
9	Hypothetical protein YdfO	[U-5% 13C; U-15N]	0.74 mM
10	NaN3		0.02 %
11	DTT		10 mM
12	CaCl2		5 mM
13	NaCl		100 mM
14	ammonium acetate		20 mM
15	D2O		5 %
16	H2O		95 %

Sample #3

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
17	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
18	NaN3		0.02 %
19	DTT		10 mM
20	CaCl2		5 mM
21	NaCl		100 mM
22	ammonium acetate		20 mM
23	D2O		99.9 %

2 3D 15N-separated NOESY

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
2	NaN3		0.02 %
3	DTT		10 mM
4	CaCl2		5 mM
5	NaCl		100 mM
6	ammonium acetate		20 mM
7	D2O		5 %
8	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
9	Hypothetical protein YdfO	[U-5% 13C; U-15N]	0.74 mM
10	NaN3		0.02 %
11	DTT		10 mM
12	CaCl2		5 mM
13	NaCl		100 mM
14	ammonium acetate		20 mM
15	D2O		5 %
16	H2O		95 %

Sample #3

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
17	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
18	NaN3		0.02 %
19	DTT		10 mM
20	CaCl2		5 mM
21	NaCl		100 mM
22	ammonium acetate		20 mM
23	D2O		99.9 %

3 HcCH-TOCSY

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
2	NaN3		0.02 %
3	DTT		10 mM
4	CaCl2		5 mM
5	NaCl		100 mM
6	ammonium acetate		20 mM
7	D2O		5 %
8	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
9	Hypothetical protein YdfO	[U-5% 13C; U-15N]	0.74 mM
10	NaN3		0.02 %
11	DTT		10 mM
12	CaCl2		5 mM
13	NaCl		100 mM
14	ammonium acetate		20 mM
15	D2O		5 %
16	H2O		95 %

Sample #3

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
17	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
18	NaN3		0.02 %
19	DTT		10 mM
20	CaCl2		5 mM
21	NaCl		100 mM
22	ammonium acetate		20 mM
23	D2O		99.9 %

4 HcCH-COSY

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
2	NaN3		0.02 %
3	DTT		10 mM
4	CaCl2		5 mM
5	NaCl		100 mM
6	ammonium acetate		20 mM
7	D2O		5 %
8	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
9	Hypothetical protein YdfO	[U-5% 13C; U-15N]	0.74 mM
10	NaN3		0.02 %
11	DTT		10 mM
12	CaCl2		5 mM
13	NaCl		100 mM
14	ammonium acetate		20 mM
15	D2O		5 %
16	H2O		95 %

Sample #3

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
17	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
18	NaN3		0.02 %
19	DTT		10 mM
20	CaCl2		5 mM
21	NaCl		100 mM
22	ammonium acetate		20 mM
23	D2O		99.9 %

5 CccoNH-TOCSY

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
2	NaN3		0.02 %
3	DTT		10 mM
4	CaCl2		5 mM
5	NaCl		100 mM
6	ammonium acetate		20 mM
7	D2O		5 %
8	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
9	Hypothetical protein YdfO	[U-5% 13C; U-15N]	0.74 mM
10	NaN3		0.02 %
11	DTT		10 mM
12	CaCl2		5 mM
13	NaCl		100 mM
14	ammonium acetate		20 mM
15	D2O		5 %
16	H2O		95 %

Sample #3

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
17	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
18	NaN3		0.02 %
19	DTT		10 mM
20	CaCl2		5 mM
21	NaCl		100 mM
22	ammonium acetate		20 mM
23	D2O		99.9 %

6 3D-HNCACB

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
2	NaN3		0.02 %
3	DTT		10 mM
4	CaCl2		5 mM
5	NaCl		100 mM
6	ammonium acetate		20 mM
7	D2O		5 %
8	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
9	Hypothetical protein YdfO	[U-5% 13C; U-15N]	0.74 mM
10	NaN3		0.02 %
11	DTT		10 mM
12	CaCl2		5 mM
13	NaCl		100 mM
14	ammonium acetate		20 mM
15	D2O		5 %
16	H2O		95 %

Sample #3

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
17	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
18	NaN3		0.02 %
19	DTT		10 mM
20	CaCl2		5 mM
21	NaCl		100 mM
22	ammonium acetate		20 mM
23	D2O		99.9 %

7 HNcoCACB

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
2	NaN3		0.02 %
3	DTT		10 mM
4	CaCl2		5 mM
5	NaCl		100 mM
6	ammonium acetate		20 mM
7	D2O		5 %
8	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
9	Hypothetical protein YdfO	[U-5% 13C; U-15N]	0.74 mM
10	NaN3		0.02 %
11	DTT		10 mM
12	CaCl2		5 mM
13	NaCl		100 mM
14	ammonium acetate		20 mM
15	D2O		5 %
16	H2O		95 %

Sample #3

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
17	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
18	NaN3		0.02 %
19	DTT		10 mM
20	CaCl2		5 mM
21	NaCl		100 mM
22	ammonium acetate		20 mM
23	D2O		99.9 %

8 HBHAcoNH

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
2	NaN3		0.02 %
3	DTT		10 mM
4	CaCl2		5 mM
5	NaCl		100 mM
6	ammonium acetate		20 mM
7	D2O		5 %
8	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
9	Hypothetical protein YdfO	[U-5% 13C; U-15N]	0.74 mM
10	NaN3		0.02 %
11	DTT		10 mM
12	CaCl2		5 mM
13	NaCl		100 mM
14	ammonium acetate		20 mM
15	D2O		5 %
16	H2O		95 %

Sample #3

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
17	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
18	NaN3		0.02 %
19	DTT		10 mM
20	CaCl2		5 mM
21	NaCl		100 mM
22	ammonium acetate		20 mM
23	D2O		99.9 %

9 HNCO

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
2	NaN3		0.02 %
3	DTT		10 mM
4	CaCl2		5 mM
5	NaCl		100 mM
6	ammonium acetate		20 mM
7	D2O		5 %
8	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
9	Hypothetical protein YdfO	[U-5% 13C; U-15N]	0.74 mM
10	NaN3		0.02 %
11	DTT		10 mM
12	CaCl2		5 mM
13	NaCl		100 mM
14	ammonium acetate		20 mM
15	D2O		5 %
16	H2O		95 %

Sample #3

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
17	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
18	NaN3		0.02 %
19	DTT		10 mM
20	CaCl2		5 mM
21	NaCl		100 mM
22	ammonium acetate		20 mM
23	D2O		99.9 %

10 13C HSQC noct Stereospecific VL Me assign.

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
2	NaN3		0.02 %
3	DTT		10 mM
4	CaCl2		5 mM
5	NaCl		100 mM
6	ammonium acetate		20 mM
7	D2O		5 %
8	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
9	Hypothetical protein YdfO	[U-5% 13C; U-15N]	0.74 mM
10	NaN3		0.02 %
11	DTT		10 mM
12	CaCl2		5 mM
13	NaCl		100 mM
14	ammonium acetate		20 mM
15	D2O		5 %
16	H2O		95 %

Sample #3

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
17	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
18	NaN3		0.02 %
19	DTT		10 mM
20	CaCl2		5 mM
21	NaCl		100 mM
22	ammonium acetate		20 mM
23	D2O		99.9 %

11 Het-NOE

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
2	NaN3		0.02 %
3	DTT		10 mM
4	CaCl2		5 mM
5	NaCl		100 mM
6	ammonium acetate		20 mM
7	D2O		5 %
8	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
9	Hypothetical protein YdfO	[U-5% 13C; U-15N]	0.74 mM
10	NaN3		0.02 %
11	DTT		10 mM
12	CaCl2		5 mM
13	NaCl		100 mM
14	ammonium acetate		20 mM
15	D2O		5 %
16	H2O		95 %

Sample #3

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
17	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
18	NaN3		0.02 %
19	DTT		10 mM
20	CaCl2		5 mM
21	NaCl		100 mM
22	ammonium acetate		20 mM
23	D2O		99.9 %

12 T1/T1rho

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
2	NaN3		0.02 %
3	DTT		10 mM
4	CaCl2		5 mM
5	NaCl		100 mM
6	ammonium acetate		20 mM
7	D2O		5 %
8	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
9	Hypothetical protein YdfO	[U-5% 13C; U-15N]	0.74 mM
10	NaN3		0.02 %
11	DTT		10 mM
12	CaCl2		5 mM
13	NaCl		100 mM
14	ammonium acetate		20 mM
15	D2O		5 %
16	H2O		95 %

Sample #3

Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
17	Hypothetical protein YdfO	[U-13C; U-15N]	0.69 mM
18	NaN3		0.02 %
19	DTT		10 mM
20	CaCl2		5 mM
21	NaCl		100 mM
22	ammonium acetate		20 mM
23	D2O		99.9 %

nullKeywords AutoStructure, ER251, NESG, NMR structure, Northeast Structural Genomics Consortium, Protein Structure Initiative, PSI-2

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Found 1 Document (1.678 seconds)

BMRB: 7274

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Hypothetical protein YdfO, : 1 : 2 : 8 entities Detail

Experiments performed 12 experiments Detail

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