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Found 1 Document (1.26 seconds)

BMRB: 4293

5EW5

Assignment of 1H, 13C and 15N Signals of the DNase Domain of Colicin E9

Authors

Whittaker, S., Boetzel, R., MacDonald, C., Lian, L., James, R., Kleanthous, C., Moore, G.

Assembly

DNase domain of colicin E9

Entity

1. DNase domain of colicin E9 (polymer), 134 monomers, 15087.75 × 2 Da Detail

MESKRNKPGK ATGKGKPVGD KWLDDAGKDS GAPIPDRIAD KLRDKEFKSF DDFRKAVWEE VSKDPELSKN LNPSNKSSVS KGYSPFTPKN QQVGGRKVYE LHHDKPISQG GEVYDMDNIR VTTPKRHIDI HRGK

Total weight

30175.5 Da

Max. entity weight

15087.75 Da

Source organism

Escherichia coli

Exptl. method

NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 97.0 %, Completeness: 59.7 %, Completeness (bb): 92.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	59.7 % (945 of 1584)	54.0 % (457 of 846)	60.2 % (363 of 603)	92.6 % (125 of 135)
Backbone	92.0 % (721 of 784)	91.5 % (247 of 270)	91.3 % (356 of 390)	95.2 % (118 of 124)
Sidechain	36.6 % (337 of 922)	36.5 % (210 of 576)	35.8 % (120 of 335)	63.6 % (7 of 11)
Aromatic	3.8 % (4 of 104)	3.8 % (2 of 52)	0.0 % (0 of 50)	100.0 % (2 of 2)
Methyl	27.7 % (26 of 94)	38.3 % (18 of 47)	17.0 % (8 of 47)

1. DNase domain of colicin E9

MESKRNKPGK ATGKGKPVGD KWLDDAGKDS GAPIPDRIAD KLRDKEFKSF DDFRKAVWEE VSKDPELSKN LNPSNKSSVS KGYSPFTPKN QQVGGRKVYE LHHDKPISQG GEVYDMDNIR VTTPKRHIDI HRGK

Show sample condition

Sample #1

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
1	DNase domain of colicin E9	[U-99% 13C; U-99% 15N]	2.0 mM
2	sodium phosphate		25.0 mM
3	H20		90 %
4	D20		10 %
5	sodium azide		0.01 %

Sample #2

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
6	DNase domain of colicin E9	[U-99% 15N]	1.5 mM
7	sodium phosphate		50 mM
8	H20		90 %
9	D20		10 %
10	sodium azide		0.01 %

Chem. Shift Complete2

Sequence coverage: 44.8 %, Completeness: 43.5 %, Completeness (bb): 65.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	43.5 % (1379 of 3168)	39.5 % (668 of 1692)	44.2 % (533 of 1206)	65.9 % (178 of 270)
Backbone	65.4 % (1025 of 1568)	65.2 % (352 of 540)	64.5 % (503 of 780)	68.5 % (170 of 248)
Sidechain	28.0 % (516 of 1844)	27.5 % (317 of 1152)	28.5 % (191 of 670)	36.4 % (8 of 22)
Aromatic	6.7 % (14 of 208)	6.7 % (7 of 104)	4.0 % (4 of 100)	75.0 % (3 of 4)
Methyl	23.9 % (45 of 188)	30.9 % (29 of 94)	17.0 % (16 of 94)

1. DNase domain of colicin E9

MESKRNKPGK ATGKGKPVGD KWLDDAGKDS GAPIPDRIAD KLRDKEFKSF DDFRKAVWEE VSKDPELSKN LNPSNKSSVS KGYSPFTPKN QQVGGRKVYE LHHDKPISQG GEVYDMDNIR VTTPKRHIDI HRGK

Show sample condition

Sample #1

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
1	DNase domain of colicin E9	[U-99% 13C; U-99% 15N]	2.0 mM
2	sodium phosphate		25.0 mM
3	H20		90 %
4	D20		10 %
5	sodium azide		0.01 %

Sample #2

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
6	DNase domain of colicin E9	[U-99% 15N]	1.5 mM
7	sodium phosphate		50 mM
8	H20		90 %
9	D20		10 %
10	sodium azide		0.01 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl protons	0.0 ppm	external	indirect	0.2514495
¹H	Dioxane	methylene protons	3.77 ppm	internal	direct	1.0
¹⁵N	TSP	methyl protons	0.0 ppm	external	indirect	0.101329

Referencing offset: 0.85 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl protons	0.0 ppm	external	indirect	0.2514495
¹H	Dioxane	methylene protons	3.77 ppm	internal	direct	1.0
¹⁵N	TSP	methyl protons	0.0 ppm	external	indirect	0.101329

Referencing offset: 0.85 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl protons	0.0 ppm	external	indirect	0.2514495
¹H	Dioxane	methylene protons	3.77 ppm	internal	direct	1.0
¹⁵N	TSP	methyl protons	0.0 ppm	external	indirect	0.101329

Referencing offset: -0.03 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl protons	0.0 ppm	external	indirect	0.2514495
¹H	Dioxane	methylene protons	3.77 ppm	internal	direct	1.0
¹⁵N	TSP	methyl protons	0.0 ppm	external	indirect	0.101329

Referencing offset: -0.05 ppm, Outliers: 2 Detail

Release date

1999-03-08

Citation 1

Assignment of 1H, 13C and 15N signals of the DNase domain of colicin E9
Whittaker, S., Boetzel, R., MacDonald, C., Lian, L., James, R., Kleanthous, C., Moore, G.
J. Biomol. NMR (1999), 14, 201-202, PubMed 10610142 , DOI: , Abstract

Show more 3 citaions

Citation 2

NMRPipe: a multidimensional spectral processing system based on UNIX pipes
Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., Bax, A.
J. Biomol. NMR (1995), 6, 277-293, PubMed 8520220 , Abstract

Citation 3

The program XEASY for computer-supported NMR spectral analysis of biological macromolecules
J. Biomol. NMR (1995), 6, 1-10, PubMed 22911575 , DOI 10.1007/BF00417486 , Abstract

Citation 4

Complete nucleotide sequence of the colicin E9 (cei) gene
Eaton, T., James, R.
Nucleic Acids Res. (1989), 17, 1761-1761, PubMed 2646600 , DOI: , Abstract

Hide non-primary 3 citaions

Related entities 1. DNase domain of colicin E9, : 1 : 10 : 10 : 29 entities Detail

Interaction partners 1. DNase domain of colicin E9, : 4 interactors Detail

More details for 4 interactors identified by 4 citations

Experiments performed 9 experiments Detail

1 1H-15N HSQC

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker DMX (500 MHz)

Sample #1

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
1	DNase domain of colicin E9	[U-99% 13C; U-99% 15N]	2.0 mM
2	sodium phosphate		25.0 mM
3	H20		90 %
4	D20		10 %
5	sodium azide		0.01 %

Sample #2

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
6	DNase domain of colicin E9	[U-99% 15N]	1.5 mM
7	sodium phosphate		50 mM
8	H20		90 %
9	D20		10 %
10	sodium azide		0.01 %

2 1H-15N NOESY-HSQC

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker DMX (500 MHz)

Sample #1

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
1	DNase domain of colicin E9	[U-99% 13C; U-99% 15N]	2.0 mM
2	sodium phosphate		25.0 mM
3	H20		90 %
4	D20		10 %
5	sodium azide		0.01 %

Sample #2

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
6	DNase domain of colicin E9	[U-99% 15N]	1.5 mM
7	sodium phosphate		50 mM
8	H20		90 %
9	D20		10 %
10	sodium azide		0.01 %

3 1H-15N TOCSY-HSQC

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker DMX (500 MHz)

Sample #1

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
1	DNase domain of colicin E9	[U-99% 13C; U-99% 15N]	2.0 mM
2	sodium phosphate		25.0 mM
3	H20		90 %
4	D20		10 %
5	sodium azide		0.01 %

Sample #2

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
6	DNase domain of colicin E9	[U-99% 15N]	1.5 mM
7	sodium phosphate		50 mM
8	H20		90 %
9	D20		10 %
10	sodium azide		0.01 %

4 HNCO

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker DMX (500 MHz)

Sample #1

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
1	DNase domain of colicin E9	[U-99% 13C; U-99% 15N]	2.0 mM
2	sodium phosphate		25.0 mM
3	H20		90 %
4	D20		10 %
5	sodium azide		0.01 %

Sample #2

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
6	DNase domain of colicin E9	[U-99% 15N]	1.5 mM
7	sodium phosphate		50 mM
8	H20		90 %
9	D20		10 %
10	sodium azide		0.01 %

5 HNCA

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker DMX (500 MHz)

Sample #1

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
1	DNase domain of colicin E9	[U-99% 13C; U-99% 15N]	2.0 mM
2	sodium phosphate		25.0 mM
3	H20		90 %
4	D20		10 %
5	sodium azide		0.01 %

Sample #2

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
6	DNase domain of colicin E9	[U-99% 15N]	1.5 mM
7	sodium phosphate		50 mM
8	H20		90 %
9	D20		10 %
10	sodium azide		0.01 %

6 HN(CO)CA

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker DMX (500 MHz)

Sample #1

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
1	DNase domain of colicin E9	[U-99% 13C; U-99% 15N]	2.0 mM
2	sodium phosphate		25.0 mM
3	H20		90 %
4	D20		10 %
5	sodium azide		0.01 %

Sample #2

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
6	DNase domain of colicin E9	[U-99% 15N]	1.5 mM
7	sodium phosphate		50 mM
8	H20		90 %
9	D20		10 %
10	sodium azide		0.01 %

7 CBCA(CO)NH

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker DMX (500 MHz)

Sample #1

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
1	DNase domain of colicin E9	[U-99% 13C; U-99% 15N]	2.0 mM
2	sodium phosphate		25.0 mM
3	H20		90 %
4	D20		10 %
5	sodium azide		0.01 %

Sample #2

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
6	DNase domain of colicin E9	[U-99% 15N]	1.5 mM
7	sodium phosphate		50 mM
8	H20		90 %
9	D20		10 %
10	sodium azide		0.01 %

8 CBCANH

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker DMX (500 MHz)

Sample #1

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
1	DNase domain of colicin E9	[U-99% 13C; U-99% 15N]	2.0 mM
2	sodium phosphate		25.0 mM
3	H20		90 %
4	D20		10 %
5	sodium azide		0.01 %

Sample #2

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
6	DNase domain of colicin E9	[U-99% 15N]	1.5 mM
7	sodium phosphate		50 mM
8	H20		90 %
9	D20		10 %
10	sodium azide		0.01 %

9 HBHA(CBCACO)NH

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker DMX (500 MHz)

Sample #1

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
1	DNase domain of colicin E9	[U-99% 13C; U-99% 15N]	2.0 mM
2	sodium phosphate		25.0 mM
3	H20		90 %
4	D20		10 %
5	sodium azide		0.01 %

Sample #2

Temperature 293 (±1) K, pH 6.2 (±0.2)

#	Name	Isotope labeling	Concentration
6	DNase domain of colicin E9	[U-99% 15N]	1.5 mM
7	sodium phosphate		50 mM
8	H20		90 %
9	D20		10 %
10	sodium azide		0.01 %

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr4293_3.str
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

Content subtype: bmr4293_3.str

#	Content subtype	Saveframe	Status	# of rows	Sequence coverage (%)
1	Assigned chemical shifts	chemical_shift_assignments_for_major_conformer_of_E9_DNase	Warning	931	96.3 (chain: 1, length: 134)
2	Assigned chemical shifts	chemical_shift_assignments_for_minor_conformer_of_E9_DNase	OK	270	30.6 (chain: 1, length: 134)
1	Chemical shift references	chemical_shift_reference_one	OK	3	No information

Assigned chemical shifts

Saveframe: chemical_shift_assignments_for_major_conformer_of_E9_DNase
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 134, Sequence coverage: 96.3%
- Total number of assignments
  - ¹H chemical shifts: 451
  - ¹³C chemical shifts: 358
  - ¹⁵N chemical shifts: 122
- Completeness of assignments
  - Entity_assemble_ID: 1
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1
Saveframe: chemical_shift_assignments_for_minor_conformer_of_E9_DNase
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 134, Sequence coverage: 30.6%
- Total number of assignments
  - ¹³C chemical shifts: 102
  - ¹H chemical shifts: 129
  - ¹⁵N chemical shifts: 39
- Completeness of assignments
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
6	ASN	CG	177.0
70	ASN	CG	176.8
90	ASN	CG	176.7
118	ASN	CG	178.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	846	423	50.0
¹³C chemical shifts	603	354	58.7
¹⁵N chemical shifts	143	122	85.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	270	244	90.4
¹³C chemical shifts	268	242	90.3
¹⁵N chemical shifts	124	116	93.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	576	179	31.1
¹³C chemical shifts	335	112	33.4
¹⁵N chemical shifts	19	6	31.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	14	28.6
¹³C chemical shifts	49	5	10.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	2	3.8
¹³C chemical shifts	50	0	0.0
¹⁵N chemical shifts	2	2	100.0

Keywords chemical exchange, colicin, EXSY

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Found 1 Document (1.26 seconds)

BMRB: 4293

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. DNase domain of colicin E9, : 1 : 10 : 10 : 29 entities Detail

Interaction partners 1. DNase domain of colicin E9, : 4 interactors Detail

Experiments performed 9 experiments Detail

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Chemical shift validation 4 contents Detail