BMRBj - BMREntryMaster

Found 1 Document (2.273 seconds)

BMRB: 7261

2HJJ

Solution NMR structure of protein ykfF from Escherichia coli. Northeast Structural Genomics target ER397. (CASP Target)

Authors

Swapna, G.V.T., Aramini, J.M., Zhao, L., Cunningham, K., Janjua, H., Ma, L., Xiao, R., Baran, M.C., Acton, T.B., Liu, J., Rost, B., Montelione, G.T.

Assembly

Hypothetical protein ykfF

Entity

1. Hypothetical protein ykfF (polymer, Thiol state: not present), 87 monomers, 10079.04 Da Detail

MTQSVLLPPG PFTRRQAQAV TTTYSNITLE DDQGSHFRLV VRDTEGRMVW RAWNFEPDAG EGLNRYIRTS GIRTDTATRL EHHHHHH

Formula weight

10079.04 Da

Source organism

Escherichia coli

Exptl. method

NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.4 %, Completeness: 90.9 %, Completeness (bb): 91.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.9 % (910 of 1001)	90.9 % (471 of 518)	90.0 % (352 of 391)	94.6 % (87 of 92)
Backbone	91.2 % (469 of 514)	90.9 % (160 of 176)	90.6 % (231 of 255)	94.0 % (78 of 83)
Sidechain	91.4 % (519 of 568)	90.9 % (311 of 342)	91.7 % (199 of 217)	100.0 % (9 of 9)
Aromatic	75.5 % (74 of 98)	75.5 % (37 of 49)	74.5 % (35 of 47)	100.0 % (2 of 2)
Methyl	100.0 % (88 of 88)	100.0 % (44 of 44)	100.0 % (44 of 44)

1. Hypothetical protein ykfF

MTQSVLLPPG PFTRRQAQAV TTTYSNITLE DDQGSHFRLV VRDTEGRMVW RAWNFEPDAG EGLNRYIRTS GIRTDTATRL EHHHHHH

Show sample condition

Sample

Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein ykfF	[U-13C; U-15N]	0.95 mM
2	CaCl2		5 mM
3	NaCl		100 mM
4	NH4OAc		20 mM
5	DTT		10 mM
6	NaN3		0.02 %
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	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.07 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: -0.07 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: -0.1 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: -0.29 ppm, Outliers: 5 Detail

Protein Blocks Logo

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

Release date

2007-04-23

Citation

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

Related entities 1. Hypothetical protein ykfF, : 1 : 2 entities Detail

Experiments performed 6 experiments Detail

1 3D 13C-separated NOESY

Instrument

#1 Model Bruker AVANCE (800 MHz)

#2 Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein ykfF	[U-13C; U-15N]	0.95 mM
2	CaCl2		5 mM
3	NaCl		100 mM
4	NH4OAc		20 mM
5	DTT		10 mM
6	NaN3		0.02 %
7	D2O		5 %
8	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Concentration
9	Hypothetical protein ykfF	[U-13C; U-15N]	0.95 mM
10	CaCl2		5 mM
11	NaCl		100 mM
12	NH4OAc		20 mM
13	DTT		10 mM
14	NaN3		0.02 %
15	D2O		100 %

Sample #3

Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Concentration
16	Hypothetical protein ykfF	[U-5% 13C; U-15N]	0.95 mM
17	CaCl2		5 mM
18	NaCl		100 mM
19	NH4OAc		20 mM
20	DTT		10 mM
21	NaN3		0.02 %
22	D2O		5 %
23	H2O		95 %

2 3D 15N-separated NOESY

Instrument

#1 Model Bruker AVANCE (800 MHz)

#2 Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein ykfF	[U-13C; U-15N]	0.95 mM
2	CaCl2		5 mM
3	NaCl		100 mM
4	NH4OAc		20 mM
5	DTT		10 mM
6	NaN3		0.02 %
7	D2O		5 %
8	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Concentration
9	Hypothetical protein ykfF	[U-13C; U-15N]	0.95 mM
10	CaCl2		5 mM
11	NaCl		100 mM
12	NH4OAc		20 mM
13	DTT		10 mM
14	NaN3		0.02 %
15	D2O		100 %

Sample #3

Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Concentration
16	Hypothetical protein ykfF	[U-5% 13C; U-15N]	0.95 mM
17	CaCl2		5 mM
18	NaCl		100 mM
19	NH4OAc		20 mM
20	DTT		10 mM
21	NaN3		0.02 %
22	D2O		5 %
23	H2O		95 %

3 HNHA

Instrument

#1 Model Bruker AVANCE (800 MHz)

#2 Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein ykfF	[U-13C; U-15N]	0.95 mM
2	CaCl2		5 mM
3	NaCl		100 mM
4	NH4OAc		20 mM
5	DTT		10 mM
6	NaN3		0.02 %
7	D2O		5 %
8	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Concentration
9	Hypothetical protein ykfF	[U-13C; U-15N]	0.95 mM
10	CaCl2		5 mM
11	NaCl		100 mM
12	NH4OAc		20 mM
13	DTT		10 mM
14	NaN3		0.02 %
15	D2O		100 %

Sample #3

Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Concentration
16	Hypothetical protein ykfF	[U-5% 13C; U-15N]	0.95 mM
17	CaCl2		5 mM
18	NaCl		100 mM
19	NH4OAc		20 mM
20	DTT		10 mM
21	NaN3		0.02 %
22	D2O		5 %
23	H2O		95 %

4 high resolution CH-HSQC (stereospecific assignment of Val/Leu methyls)

Instrument

#1 Model Bruker AVANCE (800 MHz)

#2 Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein ykfF	[U-13C; U-15N]	0.95 mM
2	CaCl2		5 mM
3	NaCl		100 mM
4	NH4OAc		20 mM
5	DTT		10 mM
6	NaN3		0.02 %
7	D2O		5 %
8	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Concentration
9	Hypothetical protein ykfF	[U-13C; U-15N]	0.95 mM
10	CaCl2		5 mM
11	NaCl		100 mM
12	NH4OAc		20 mM
13	DTT		10 mM
14	NaN3		0.02 %
15	D2O		100 %

Sample #3

Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Concentration
16	Hypothetical protein ykfF	[U-5% 13C; U-15N]	0.95 mM
17	CaCl2		5 mM
18	NaCl		100 mM
19	NH4OAc		20 mM
20	DTT		10 mM
21	NaN3		0.02 %
22	D2O		5 %
23	H2O		95 %

5 3D GFT backbone expts

Instrument

#1 Model Bruker AVANCE (800 MHz)

#2 Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein ykfF	[U-13C; U-15N]	0.95 mM
2	CaCl2		5 mM
3	NaCl		100 mM
4	NH4OAc		20 mM
5	DTT		10 mM
6	NaN3		0.02 %
7	D2O		5 %
8	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Concentration
9	Hypothetical protein ykfF	[U-13C; U-15N]	0.95 mM
10	CaCl2		5 mM
11	NaCl		100 mM
12	NH4OAc		20 mM
13	DTT		10 mM
14	NaN3		0.02 %
15	D2O		100 %

Sample #3

Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Concentration
16	Hypothetical protein ykfF	[U-5% 13C; U-15N]	0.95 mM
17	CaCl2		5 mM
18	NaCl		100 mM
19	NH4OAc		20 mM
20	DTT		10 mM
21	NaN3		0.02 %
22	D2O		5 %
23	H2O		95 %

6 3D HCCH-COSY and HCCH-TOCSYs

Instrument

#1 Model Bruker AVANCE (800 MHz)

#2 Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Concentration
1	Hypothetical protein ykfF	[U-13C; U-15N]	0.95 mM
2	CaCl2		5 mM
3	NaCl		100 mM
4	NH4OAc		20 mM
5	DTT		10 mM
6	NaN3		0.02 %
7	D2O		5 %
8	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Concentration
9	Hypothetical protein ykfF	[U-13C; U-15N]	0.95 mM
10	CaCl2		5 mM
11	NaCl		100 mM
12	NH4OAc		20 mM
13	DTT		10 mM
14	NaN3		0.02 %
15	D2O		100 %

Sample #3

Pressure 1 atm, Temperature 293 K, pH 5.5

#	Name	Isotope labeling	Concentration
16	Hypothetical protein ykfF	[U-5% 13C; U-15N]	0.95 mM
17	CaCl2		5 mM
18	NaCl		100 mM
19	NH4OAc		20 mM
20	DTT		10 mM
21	NaN3		0.02 %
22	D2O		5 %
23	H2O		95 %

nullKeywords ER397, NMR structure, Northeast Structural Genomics Consortium (NESG), Protein Structure Initiative, PSI-2

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Found 1 Document (2.273 seconds)

BMRB: 7261

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Hypothetical protein ykfF, : 1 : 2 entities Detail

Experiments performed 6 experiments Detail

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