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Found 1 Document (1.635 seconds)

BMRB: 6362

2AZH

Solution structure of Iron-Sulfur cluster assembly protein IscU from Bacillus subtilis, with Zinc bound at the active site. Northeast Structural Genomics Consortium Target SR17

Authors

Kornhaber, G.J., Swapna, G.V., Ramelot, T.A., Cort, J.R., Kennedy, M.A., Montelione, G.T.

Assembly

NifU-like protein

Entity

1. NifU-like protein (polymer, Thiol state: all other bound), 147 monomers, 16166.32 Da Detail

MSFNANLDTL YRQVIMDHYK NPRNKGVLND SIVVDMNNPT CGDRIRLTMK LDGDIVEDAK FEGEGCSISM ASASMMTQAI KGKDIETALS MSKIFSDMMQ GKEYDDSIDL GDIEALQGVS KFPARIKCAT LSWKALEKGV AKEEGGN

2. ZN (non-polymer), 65.409 Da

Total weight

16231.7295 Da

Max. entity weight

16166.32 Da

Entity Connection

na 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS41:SG	2:ZN1:ZN
2	na	sing	1:CYS66:SG	2:ZN1:ZN
3	na	sing	1:CYS128:SG	2:ZN1:ZN
4	na	sing	1:ASP43:OD1	2:ZN1:ZN

Source organism

Bacillus subtilis

Exptl. method

NMR

Refine. method

Minimal constraint structure contained 492 conformationally restricting NOE-derived distance constraints, 108 hydrogen bond constraints, and 197 dihedral angle constraints. This resulted in 5.9 constraints per residue and 1.2 long range constraints per residue. Structure determination was performed

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.0 %, Completeness: 45.6 %, Completeness (bb): 66.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	45.6 % (758 of 1663)	31.0 % (269 of 867)	53.8 % (344 of 639)	92.4 % (145 of 157)
Backbone	66.2 % (580 of 876)	50.2 % (152 of 303)	68.1 % (292 of 429)	94.4 % (136 of 144)
Sidechain	33.5 % (309 of 922)	20.7 % (117 of 564)	53.3 % (184 of 345)	61.5 % (8 of 13)
Aromatic	18.8 % (15 of 80)	35.0 % (14 of 40)	2.6 % (1 of 39)	0.0 % (0 of 1)
Methyl	62.3 % (91 of 146)	54.8 % (40 of 73)	69.9 % (51 of 73)

1. NifU-like protein

MSFNANLDTL YRQVIMDHYK NPRNKGVLND SIVVDMNNPT CGDRIRLTMK LDGDIVEDAK FEGEGCSISM ASASMMTQAI KGKDIETALS MSKIFSDMMQ GKEYDDSIDL GDIEALQGVS KFPARIKCAT LSWKALEKGV AKEEGGN

Show sample condition

Sample #1

Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	NifU-like protein	[U-13C; U-15N; U-2H; NA-V,L,I-methyl]	0.7 mM
2	Potassium Phosphate		100 mM
3	Glycerol		200 mM
4	DTT		1 mM
5	NaN3		0.02 %
6	D2O		5 %
7	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	NifU-like protein	[U-13C; NA-Y,F; U-15N; U-2H; NA-Y,F]	0.4 mM
9	Sodium Phosphate		20 mM
10	Sodium Chloride		50 mM
11	DTT		10 mM
12	NaN3		0.02 %
13	D2O		5 %
14	H2O		95 %

LACS Plot; CA

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

Referencing offset: 0.29 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.29 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 1XJS, Strand ID: A Detail

Release date

2005-11-06

Citation

Solution NMR structure of the iron-sulfur cluster assembly protein U (IscU) with zinc bound at the active site
Ramelot, T.A., Cort, J.R., Goldsmith-Fischman, S., Kornhaber, G.J., Xiao, R., Shastry, R., Acton, T.B., Honig, B., Montelione, G.T., Kennedy, M.A.
J. Mol. Biol. (2004), 344, 567-583, PubMed 15522305 , DOI 10.1016/j.jmb.2004.08.038 , Abstract

Related entities 1. NifU-like protein, : 1 : 6 : 2 : 63 entities Detail

Interaction partners 1. NifU-like protein, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 8 experiments Detail

1 3D-TOCSYS

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	NifU-like protein	[U-13C; U-15N; U-2H; NA-V,L,I-methyl]	0.7 mM
2	Potassium Phosphate		100 mM
3	Glycerol		200 mM
4	DTT		1 mM
5	NaN3		0.02 %
6	D2O		5 %
7	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	NifU-like protein	[U-13C; NA-Y,F; U-15N; U-2H; NA-Y,F]	0.4 mM
9	Sodium Phosphate		20 mM
10	Sodium Chloride		50 mM
11	DTT		10 mM
12	NaN3		0.02 %
13	D2O		5 %
14	H2O		95 %

2 13C,1H-HSQC

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	NifU-like protein	[U-13C; U-15N; U-2H; NA-V,L,I-methyl]	0.7 mM
2	Potassium Phosphate		100 mM
3	Glycerol		200 mM
4	DTT		1 mM
5	NaN3		0.02 %
6	D2O		5 %
7	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	NifU-like protein	[U-13C; NA-Y,F; U-15N; U-2H; NA-Y,F]	0.4 mM
9	Sodium Phosphate		20 mM
10	Sodium Chloride		50 mM
11	DTT		10 mM
12	NaN3		0.02 %
13	D2O		5 %
14	H2O		95 %

3 15N,1H-HSQC

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	NifU-like protein	[U-13C; U-15N; U-2H; NA-V,L,I-methyl]	0.7 mM
2	Potassium Phosphate		100 mM
3	Glycerol		200 mM
4	DTT		1 mM
5	NaN3		0.02 %
6	D2O		5 %
7	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	NifU-like protein	[U-13C; NA-Y,F; U-15N; U-2H; NA-Y,F]	0.4 mM
9	Sodium Phosphate		20 mM
10	Sodium Chloride		50 mM
11	DTT		10 mM
12	NaN3		0.02 %
13	D2O		5 %
14	H2O		95 %

4 2D Homonuclear NOESY

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	NifU-like protein	[U-13C; U-15N; U-2H; NA-V,L,I-methyl]	0.7 mM
2	Potassium Phosphate		100 mM
3	Glycerol		200 mM
4	DTT		1 mM
5	NaN3		0.02 %
6	D2O		5 %
7	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	NifU-like protein	[U-13C; NA-Y,F; U-15N; U-2H; NA-Y,F]	0.4 mM
9	Sodium Phosphate		20 mM
10	Sodium Chloride		50 mM
11	DTT		10 mM
12	NaN3		0.02 %
13	D2O		5 %
14	H2O		95 %

5 4D 13C-separated NOESY

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	NifU-like protein	[U-13C; U-15N; U-2H; NA-V,L,I-methyl]	0.7 mM
2	Potassium Phosphate		100 mM
3	Glycerol		200 mM
4	DTT		1 mM
5	NaN3		0.02 %
6	D2O		5 %
7	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	NifU-like protein	[U-13C; NA-Y,F; U-15N; U-2H; NA-Y,F]	0.4 mM
9	Sodium Phosphate		20 mM
10	Sodium Chloride		50 mM
11	DTT		10 mM
12	NaN3		0.02 %
13	D2O		5 %
14	H2O		95 %

6 3D 13C-separated NOESY

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	NifU-like protein	[U-13C; U-15N; U-2H; NA-V,L,I-methyl]	0.7 mM
2	Potassium Phosphate		100 mM
3	Glycerol		200 mM
4	DTT		1 mM
5	NaN3		0.02 %
6	D2O		5 %
7	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	NifU-like protein	[U-13C; NA-Y,F; U-15N; U-2H; NA-Y,F]	0.4 mM
9	Sodium Phosphate		20 mM
10	Sodium Chloride		50 mM
11	DTT		10 mM
12	NaN3		0.02 %
13	D2O		5 %
14	H2O		95 %

7 3D 15N-separated NOESY

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	NifU-like protein	[U-13C; U-15N; U-2H; NA-V,L,I-methyl]	0.7 mM
2	Potassium Phosphate		100 mM
3	Glycerol		200 mM
4	DTT		1 mM
5	NaN3		0.02 %
6	D2O		5 %
7	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	NifU-like protein	[U-13C; NA-Y,F; U-15N; U-2H; NA-Y,F]	0.4 mM
9	Sodium Phosphate		20 mM
10	Sodium Chloride		50 mM
11	DTT		10 mM
12	NaN3		0.02 %
13	D2O		5 %
14	H2O		95 %

8 H/D exchange

Instrument

Model Varian INOVA (600 MHz)

Sample #1

Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	NifU-like protein	[U-13C; U-15N; U-2H; NA-V,L,I-methyl]	0.7 mM
2	Potassium Phosphate		100 mM
3	Glycerol		200 mM
4	DTT		1 mM
5	NaN3		0.02 %
6	D2O		5 %
7	H2O		95 %

Sample #2

Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	NifU-like protein	[U-13C; NA-Y,F; U-15N; U-2H; NA-Y,F]	0.4 mM
9	Sodium Phosphate		20 mM
10	Sodium Chloride		50 mM
11	DTT		10 mM
12	NaN3		0.02 %
13	D2O		5 %
14	H2O		95 %

nullKeywords SR17, NMR Structure, Autostructure, Iron-Sulfur, Zinc, Northeast Structural Genomics Consortium, NESG, NIFU-LIKE, Protein Structure Initiative, Structural Genomics

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Found 1 Document (1.635 seconds)

BMRB: 6362

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Chemical shift reference

Chemical shift reference

Related entities 1. NifU-like protein, : 1 : 6 : 2 : 63 entities Detail

Interaction partners 1. NifU-like protein, : 1 interactors Detail

Experiments performed 8 experiments Detail

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