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BMRB: 5819

3BVD

Complete 1H, 15N and 13C assignment of the soluble domain of the ba3 oxidase subunit II of Thermus thermophilus in the reduced state

Authors

Mukrasch, M.D., Luecke, C., Loehr, F., Maneg, O., Ludwig, B., Rueterjans, H.

Assembly

CuA domain

Entity

1. CuA domain (polymer, Thiol state: all other bound), 136 monomers, 14934.81 Da Detail

MAYTLATHTA GVIPAGKLER VDPTTVRQEG PWADPAQAVV QTGPNQYTVY VLAFAFGYQP NPIEVPQGAE IVFKITSPDV IHGFHVEGTN INVEVLPGEV STVRYTFKRP GEYRIICNQY CGLGHQNMFG TIVVKE

2. CU1 (non-polymer), 63.546 × 2 Da

Total weight

15061.901 Da

Max. entity weight

14934.81 Da

Entity Connection

na 8 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:HIS125:ND1	2:CU11:CU
2	na	sing	1:GLN119:OE1	2:CU11:CU
3	na	sing	1:CYS117:SG	2:CU11:CU
4	na	sing	1:CYS121:SG	2:CU11:CU
5	na	sing	1:HIS82:ND1	2:CU11:CU
6	na	sing	1:MET128:SD	2:CU11:CU
7	na	sing	1:CYS117:SG	2:CU11:CU
8	na	sing	1:CYS121:SG	2:CU11:CU

Source organism

Thermus thermophilus

Exptl. method

NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 97.1 %, Completeness: 89.4 %, Completeness (bb): 95.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.4 % (1396 of 1561)	91.5 % (734 of 802)	86.6 % (536 of 619)	90.0 % (126 of 140)
Backbone	95.0 % (754 of 794)	93.8 % (257 of 274)	95.7 % (378 of 395)	95.2 % (119 of 125)
Sidechain	85.4 % (760 of 890)	90.3 % (477 of 528)	79.5 % (276 of 347)	46.7 % (7 of 15)
Aromatic	54.2 % (78 of 144)	91.7 % (66 of 72)	15.5 % (11 of 71)	100.0 % (1 of 1)
Methyl	97.6 % (164 of 168)	96.4 % (81 of 84)	98.8 % (83 of 84)

1. CuA domain

MAYTLATHTA GVIPAGKLER VDPTTVRQEG PWADPAQAVV QTGPNQYTVY VLAFAFGYQP NPIEVPQGAE IVFKITSPDV IHGFHVEGTN INVEVLPGEV STVRYTFKRP GEYRIICNQY CGLGHQNMFG TIVVKE

Show sample condition

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	CuA domain	[U-98% 15N]	1.2 mM
2	potassium phosphate		20 mM
3	ascorbate		5 mM
4	Pefabloc		0.1 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
5	CuA domain	[U-99% 13C; U-98% 15N]	0.9 mM
6	potassium phosphate		20 mM
7	ascorbate		10 mM
8	Pefabloc		0.1 mM

Sample #3

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Concentration
9	CuA domain	2.0 mM
10	potassium phosphate	20 mM
11	ascorbate	5 mM

Chem. Shift Complete2

Sequence coverage: 24.3 %, Completeness: 53.0 %, Completeness (bb): 57.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	53.0 % (1654 of 3122)	53.7 % (862 of 1604)	51.5 % (638 of 1238)	55.0 % (154 of 280)
Backbone	57.0 % (905 of 1588)	56.0 % (307 of 548)	57.1 % (451 of 790)	58.8 % (147 of 250)
Sidechain	49.8 % (887 of 1780)	52.2 % (551 of 1056)	47.4 % (329 of 694)	23.3 % (7 of 30)
Aromatic	33.7 % (97 of 288)	54.9 % (79 of 144)	12.0 % (17 of 142)	50.0 % (1 of 2)
Methyl	60.1 % (202 of 336)	58.3 % (98 of 168)	61.9 % (104 of 168)

1. CuA domain

MAYTLATHTA GVIPAGKLER VDPTTVRQEG PWADPAQAVV QTGPNQYTVY VLAFAFGYQP NPIEVPQGAE IVFKITSPDV IHGFHVEGTN INVEVLPGEV STVRYTFKRP GEYRIICNQY CGLGHQNMFG TIVVKE

Show sample condition

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	CuA domain	[U-98% 15N]	1.2 mM
2	potassium phosphate		20 mM
3	ascorbate		5 mM
4	Pefabloc		0.1 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
5	CuA domain	[U-99% 13C; U-98% 15N]	0.9 mM
6	potassium phosphate		20 mM
7	ascorbate		10 mM
8	Pefabloc		0.1 mM

Release date

2004-04-06

Citation 1

Complete 1H, 15N and 13C assignment of the soluble domain of the ba3 oxidase subunit II of Thermus thermophilus in the reduced state
Mukrasch, M.D., Luecke, C., Loehr, F., Maneg, O., Ludwig, B., Rueterjans, H.
J. Biomol. NMR (2004), 28, 297-298, PubMed 14752263 , DOI 10.1023/B:JNMR.0000013687.83263.b5 , Abstract

Show more 1 citaion

Citation 2

Water-soluble, recombinant CuA-domain of the cytochrome ba3 subunit II from Thermus thermophilus
Slutter, C.E., Sanders, D., Wittung, P., Malmstrom, B.G., Aasa, R., Richards, J.H., Gray, H.B., Fee, J.A.
Biochemistry (1996), 35, 3387-3395, PubMed 8639488 , DOI 10.1021/bi9525839 , Abstract

Hide non-primary 1 citaion

Related entities 1. CuA domain, : 1 : 1 : 40 : 3 : 37 entities Detail

Interaction partners 1. CuA domain, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 12 experiments Detail

1 1H-1H TOCSY

Instrument

Model Bruker DMX (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	CuA domain	[U-98% 15N]	1.2 mM
2	potassium phosphate		20 mM
3	ascorbate		5 mM
4	Pefabloc		0.1 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
5	CuA domain	[U-99% 13C; U-98% 15N]	0.9 mM
6	potassium phosphate		20 mM
7	ascorbate		10 mM
8	Pefabloc		0.1 mM

Sample #3

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Concentration
9	CuA domain	2.0 mM
10	potassium phosphate	20 mM
11	ascorbate	5 mM

2 1H-1H NOESY

Instrument

Model Bruker DMX (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	CuA domain	[U-98% 15N]	1.2 mM
2	potassium phosphate		20 mM
3	ascorbate		5 mM
4	Pefabloc		0.1 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
5	CuA domain	[U-99% 13C; U-98% 15N]	0.9 mM
6	potassium phosphate		20 mM
7	ascorbate		10 mM
8	Pefabloc		0.1 mM

Sample #3

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Concentration
9	CuA domain	2.0 mM
10	potassium phosphate	20 mM
11	ascorbate	5 mM

3 15N-1H TROSY

Instrument

Model Bruker DMX (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	CuA domain	[U-98% 15N]	1.2 mM
2	potassium phosphate		20 mM
3	ascorbate		5 mM
4	Pefabloc		0.1 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
5	CuA domain	[U-99% 13C; U-98% 15N]	0.9 mM
6	potassium phosphate		20 mM
7	ascorbate		10 mM
8	Pefabloc		0.1 mM

Sample #3

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Concentration
9	CuA domain	2.0 mM
10	potassium phosphate	20 mM
11	ascorbate	5 mM

4 15N-1H TROSY-HNCO

Instrument

Model Bruker DMX (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	CuA domain	[U-98% 15N]	1.2 mM
2	potassium phosphate		20 mM
3	ascorbate		5 mM
4	Pefabloc		0.1 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
5	CuA domain	[U-99% 13C; U-98% 15N]	0.9 mM
6	potassium phosphate		20 mM
7	ascorbate		10 mM
8	Pefabloc		0.1 mM

Sample #3

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Concentration
9	CuA domain	2.0 mM
10	potassium phosphate	20 mM
11	ascorbate	5 mM

5 15N-1H TROSY-HNCACB

Instrument

Model Bruker DMX (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	CuA domain	[U-98% 15N]	1.2 mM
2	potassium phosphate		20 mM
3	ascorbate		5 mM
4	Pefabloc		0.1 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
5	CuA domain	[U-99% 13C; U-98% 15N]	0.9 mM
6	potassium phosphate		20 mM
7	ascorbate		10 mM
8	Pefabloc		0.1 mM

Sample #3

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Concentration
9	CuA domain	2.0 mM
10	potassium phosphate	20 mM
11	ascorbate	5 mM

6 (H)CC(CO)NH-TOCSY

Instrument

Model Bruker DMX (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	CuA domain	[U-98% 15N]	1.2 mM
2	potassium phosphate		20 mM
3	ascorbate		5 mM
4	Pefabloc		0.1 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
5	CuA domain	[U-99% 13C; U-98% 15N]	0.9 mM
6	potassium phosphate		20 mM
7	ascorbate		10 mM
8	Pefabloc		0.1 mM

Sample #3

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Concentration
9	CuA domain	2.0 mM
10	potassium phosphate	20 mM
11	ascorbate	5 mM

7 H(CC)(CO)NH-TOCSY

Instrument

Model Bruker DMX (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	CuA domain	[U-98% 15N]	1.2 mM
2	potassium phosphate		20 mM
3	ascorbate		5 mM
4	Pefabloc		0.1 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
5	CuA domain	[U-99% 13C; U-98% 15N]	0.9 mM
6	potassium phosphate		20 mM
7	ascorbate		10 mM
8	Pefabloc		0.1 mM

Sample #3

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Concentration
9	CuA domain	2.0 mM
10	potassium phosphate	20 mM
11	ascorbate	5 mM

8 (HACA)CO(CA)NH

Instrument

Model Bruker DMX (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	CuA domain	[U-98% 15N]	1.2 mM
2	potassium phosphate		20 mM
3	ascorbate		5 mM
4	Pefabloc		0.1 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
5	CuA domain	[U-99% 13C; U-98% 15N]	0.9 mM
6	potassium phosphate		20 mM
7	ascorbate		10 mM
8	Pefabloc		0.1 mM

Sample #3

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Concentration
9	CuA domain	2.0 mM
10	potassium phosphate	20 mM
11	ascorbate	5 mM

9 (HM)CMC(CM)HM

Instrument

Model Bruker DMX (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	CuA domain	[U-98% 15N]	1.2 mM
2	potassium phosphate		20 mM
3	ascorbate		5 mM
4	Pefabloc		0.1 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
5	CuA domain	[U-99% 13C; U-98% 15N]	0.9 mM
6	potassium phosphate		20 mM
7	ascorbate		10 mM
8	Pefabloc		0.1 mM

Sample #3

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Concentration
9	CuA domain	2.0 mM
10	potassium phosphate	20 mM
11	ascorbate	5 mM

10 CT-13C-HSQC

Instrument

Model Bruker DMX (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	CuA domain	[U-98% 15N]	1.2 mM
2	potassium phosphate		20 mM
3	ascorbate		5 mM
4	Pefabloc		0.1 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
5	CuA domain	[U-99% 13C; U-98% 15N]	0.9 mM
6	potassium phosphate		20 mM
7	ascorbate		10 mM
8	Pefabloc		0.1 mM

Sample #3

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Concentration
9	CuA domain	2.0 mM
10	potassium phosphate	20 mM
11	ascorbate	5 mM

11 13C-1H-TROSY-HCD(CG)CB

Instrument

Model Bruker DMX (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	CuA domain	[U-98% 15N]	1.2 mM
2	potassium phosphate		20 mM
3	ascorbate		5 mM
4	Pefabloc		0.1 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
5	CuA domain	[U-99% 13C; U-98% 15N]	0.9 mM
6	potassium phosphate		20 mM
7	ascorbate		10 mM
8	Pefabloc		0.1 mM

Sample #3

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Concentration
9	CuA domain	2.0 mM
10	potassium phosphate	20 mM
11	ascorbate	5 mM

12 15N-1H HMBC

Instrument

Model Bruker DMX (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	CuA domain	[U-98% 15N]	1.2 mM
2	potassium phosphate		20 mM
3	ascorbate		5 mM
4	Pefabloc		0.1 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Concentration
5	CuA domain	[U-99% 13C; U-98% 15N]	0.9 mM
6	potassium phosphate		20 mM
7	ascorbate		10 mM
8	Pefabloc		0.1 mM

Sample #3

Temperature 298 (±0.1) K, pH 6.0 (±0.1)

#	Name	Concentration
9	CuA domain	2.0 mM
10	potassium phosphate	20 mM
11	ascorbate	5 mM

Chemical shift validation 5 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr5819_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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:125:HIS:ND1	2:1:CU1:CU	unknown	unknown	n/a
1:119:GLN:OE1	2:1:CU1:CU	unknown	unknown	n/a
1:117:CYS:SG	2:1:CU1:CU	oxidized 6.8%, reduced 93.2%, CA 59.9, CB 32.3 ppm	unknown	n/a
1:121:CYS:SG	2:1:CU1:CU	oxidized 93.4%, reduced 6.6%, CA 56.5, CB 34.5 ppm	unknown	n/a
1:82:HIS:ND1	3:1:CU1:CU	unknown	unknown	n/a
1:128:MET:SD	3:1:CU1:CU	unknown	unknown	n/a
1:117:CYS:SG	3:1:CU1:CU	oxidized 6.8%, reduced 93.2%, CA 59.9, CB 32.3 ppm	unknown	n/a
1:121:CYS:SG	3:1:CU1:CU	oxidized 93.4%, reduced 6.6%, CA 56.5, CB 34.5 ppm	unknown	n/a

Non-standard residues

None

Content subtype: bmr5819_3.str

#	Content subtype	Saveframe	Status	# of rows	Sequence coverage (%)
1	Assigned chemical shifts	shift_set_1	Warning	1603	97.8 (chain: 1, length: 136)
2	Assigned chemical shifts	shift_set_2	Warning	48	2.9 (chain: 1, length: 136)
1	Chemical shift references	chemical_shift_reference	OK	3	No information

Assigned chemical shifts

Saveframe: shift_set_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 136, Sequence coverage: 97.8%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MAYTLATHTAGVIPAGKLERVDPTTVRQEGPWADPAQAVVQTGPNQYTVYVLAFAFGYQPNPIEVPQGAEIVFKITSPDVIHGFHVEGTNINVEVLPGEV
  ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
..YTLATHTAGVIPAGKLERVDPTTVRQEGPWADPAQAVVQTG.NQYTVYVLAFAFGYQPNPIEVPQGAEIVFKITSPDVIHGFHVEGTNINVEVLPGEV

-------110-------120-------130------
STVRYTFKRPGEYRIICNQYCGLGHQNMFGTIVVKE
||||||||||||||||||||||||||||||||||||
STVRYTFKRPGEYRIICNQYCGLGHQNMFGTIVVKE

Total number of assignments
- ¹H chemical shifts: 912
- ¹³C chemical shifts: 553
- ¹⁵N chemical shifts: 138

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
8	HIS	CG	133.0
8	HIS	ND1	203.4
8	HIS	NE2	177.5
28	GLN	CD	179.9
32	TRP	CE2	139.6
37	GLN	CD	180.5
67	GLN	CD	178.4
82	HIS	HE2	11.78
82	HIS	CG	135.5
82	HIS	ND1	226.6
82	HIS	NE2	165.0
85	HIS	CG	129.8
85	HIS	ND1	174.4
85	HIS	NE2	199.0
125	HIS	CG	136.5
125	HIS	ND1	220.1
125	HIS	NE2	164.3
126	GLN	CD	180.5
127	ASN	CG	177.6

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	802	743	92.6
¹³C chemical shifts	619	543	87.7
¹⁵N chemical shifts	145	130	89.7

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	274	264	96.4
¹³C chemical shifts	272	266	97.8
¹⁵N chemical shifts	125	121	96.8

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	528	479	90.7
¹³C chemical shifts	347	277	79.8
¹⁵N chemical shifts	20	9	45.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	86	84	97.7
¹³C chemical shifts	86	84	97.7

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	67	93.1
¹³C chemical shifts	71	11	15.5
¹⁵N chemical shifts	1	1	100.0

Redox state of CYS
Peptide bond of PRO
Tautomeric state of HIS
Rotameric state of ILE , LEU, and VAL
Histogram of normalized assigned chemical shifts
Random coil index and derived parameters (S² and NMR RMSD)
- Chain_ID: 1

Saveframe: shift_set_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 136, Sequence coverage: 2.9%
- Total number of assignments
  - ¹H chemical shifts: 26
  - ¹³C chemical shifts: 19
  - ¹⁵N chemical shifts: 3
- Completeness of assignments
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Keywords CuA center, prolyl cis/trans isomerization

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Found 1 Document (1.539 seconds)

BMRB: 5819

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Related entities 1. CuA domain, : 1 : 1 : 40 : 3 : 37 entities Detail

Interaction partners 1. CuA domain, : 1 interactors Detail

Experiments performed 12 experiments Detail

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