BMRBj - BMREntryMaster

Found 1 Document (1.381 seconds)

BMRB: 5397

7BG9

1H, 13C and 15N resonance assignment of an affibody-target complex

Authors

Lendel, C., Wahlberg, E., Berglund, H., Eklund, M., Nygren, P., Hard, T.

Assembly

heterodimer of Z-domain and ZSPA-1 affibody

Entity

1. Z-domain (polymer, Thiol state: not present), 58 monomers, 6640.251 Da Detail

VDNKFNKEQQ NAFYEILHLP NLNEEQRNAF IQSLKDDPSQ SANLLAEAKK LNDAQAPK

2. ZSPA-1 (polymer, Thiol state: not present), 58 monomers, 6439.198 Da Detail

VDNKFNKELS VAGREIVTLP NLNDPQKKAF IFSLWDDPSQ SANLLAEAKK LNDAQAPK

Total weight

13079.449 Da

Max. entity weight

6640.251 Da

Exptl. method

NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 56.9 %, Completeness: 53.7 %, Completeness (bb): 55.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	53.7 % (750 of 1396)	55.3 % (408 of 738)	51.4 % (270 of 525)	54.1 % (72 of 133)
Backbone	55.0 % (375 of 682)	55.3 % (125 of 226)	55.3 % (192 of 347)	53.2 % (58 of 109)
Sidechain	53.1 % (440 of 829)	55.3 % (283 of 512)	48.8 % (143 of 293)	58.3 % (14 of 24)
Aromatic	31.0 % (26 of 84)	50.0 % (21 of 42)	12.2 % (5 of 41)	0.0 % (0 of 1)
Methyl	52.5 % (62 of 118)	52.5 % (31 of 59)	52.5 % (31 of 59)

1. Z-domain

VDNKFNKEQQ NAFYEILHLP NLNEEQRNAF IQSLKDDPSQ SANLLAEAKK LNDAQAPK

2. ZSPA-1

VDNKFNKELS VAGREIVTLP NLNDPQKKAF IFSLWDDPSQ SANLLAEAKK LNDAQAPK

Show sample condition

Sample

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
1	Z-domain	[U-13C; U-15N]	1.5 ~ 2.0 mM
2	ZSPA-1		1.65 ~ 2.5 mM
3	potassium phosphate		20 mM
4	sodium azide		0.01 %
5	D2O		10.0 ~ 100.0 %

Chem. Shift Complete2

Sequence coverage: 58.6 %, Completeness: 54.4 %, Completeness (bb): 55.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	54.4 % (1519 of 2792)	55.3 % (816 of 1476)	53.0 % (557 of 1050)	54.9 % (146 of 266)
Backbone	55.4 % (755 of 1364)	55.1 % (249 of 452)	55.8 % (387 of 694)	54.6 % (119 of 218)
Sidechain	53.9 % (894 of 1658)	55.4 % (567 of 1024)	51.2 % (300 of 586)	56.3 % (27 of 48)
Aromatic	37.5 % (63 of 168)	50.0 % (42 of 84)	24.4 % (20 of 82)	50.0 % (1 of 2)
Methyl	53.8 % (127 of 236)	53.4 % (63 of 118)	54.2 % (64 of 118)

1. Z-domain

VDNKFNKEQQ NAFYEILHLP NLNEEQRNAF IQSLKDDPSQ SANLLAEAKK LNDAQAPK

2. ZSPA-1

VDNKFNKELS VAGREIVTLP NLNDPQKKAF IFSLWDDPSQ SANLLAEAKK LNDAQAPK

Show sample condition

Sample

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
6	ZSPA-1	[U-13C; U-15N]	1.5 ~ 2.0 mM
7	Z-domain		1.65 ~ 2.5 mM
8	potassium phosphate		20 mM
9	sodium azide		0.01 %
10	D2O		10.0 ~ 100.0 %

Release date

2002-12-22

Citation

Letter to the editor: 1H, 13C and 15N resonance assignments of Aquifex aeolicus shikimate kinase in complex with the substrate shikimate
Lendel, C., Wahlberg, E., Berglund, H., Eklund, M., Nygren, P., Hard, T.
J. Biomol. NMR (2000), 17, 277-278, PubMed 10959638 , DOI: , Abstract

Related entities 1. Z-domain, : 2 : 40 : 67 : 67 entities Detail

Related entities 2. ZSPA-1, : 2 : 2 : 2 : 150 entities Detail

Interaction partners 1. Z-domain, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 10 experiments Detail

1 1H-15N HSQC

Instrument

#1 Model Bruker AVANCE (500 MHz)

#2 Model Bruker AVANCE (600 MHz)

#3 Model Varian INOVA (800 MHz)

Sample #1

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
1	Z-domain	[U-13C; U-15N]	1.5 ~ 2.0 mM
2	ZSPA-1		1.65 ~ 2.5 mM
3	potassium phosphate		20 mM
4	sodium azide		0.01 %
5	D2O		10.0 ~ 100.0 %

Sample #2

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
6	ZSPA-1	[U-13C; U-15N]	1.5 ~ 2.0 mM
7	Z-domain		1.65 ~ 2.5 mM
8	potassium phosphate		20 mM
9	sodium azide		0.01 %
10	D2O		10.0 ~ 100.0 %

2 1H-13C HSQC

Instrument

#1 Model Bruker AVANCE (500 MHz)

#2 Model Bruker AVANCE (600 MHz)

#3 Model Varian INOVA (800 MHz)

Sample #1

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
1	Z-domain	[U-13C; U-15N]	1.5 ~ 2.0 mM
2	ZSPA-1		1.65 ~ 2.5 mM
3	potassium phosphate		20 mM
4	sodium azide		0.01 %
5	D2O		10.0 ~ 100.0 %

Sample #2

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
6	ZSPA-1	[U-13C; U-15N]	1.5 ~ 2.0 mM
7	Z-domain		1.65 ~ 2.5 mM
8	potassium phosphate		20 mM
9	sodium azide		0.01 %
10	D2O		10.0 ~ 100.0 %

3 CBCA(CO)NH

Instrument

#1 Model Bruker AVANCE (500 MHz)

#2 Model Bruker AVANCE (600 MHz)

#3 Model Varian INOVA (800 MHz)

Sample #1

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
1	Z-domain	[U-13C; U-15N]	1.5 ~ 2.0 mM
2	ZSPA-1		1.65 ~ 2.5 mM
3	potassium phosphate		20 mM
4	sodium azide		0.01 %
5	D2O		10.0 ~ 100.0 %

Sample #2

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
6	ZSPA-1	[U-13C; U-15N]	1.5 ~ 2.0 mM
7	Z-domain		1.65 ~ 2.5 mM
8	potassium phosphate		20 mM
9	sodium azide		0.01 %
10	D2O		10.0 ~ 100.0 %

4 CBCANH

Instrument

#1 Model Bruker AVANCE (500 MHz)

#2 Model Bruker AVANCE (600 MHz)

#3 Model Varian INOVA (800 MHz)

Sample #1

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
1	Z-domain	[U-13C; U-15N]	1.5 ~ 2.0 mM
2	ZSPA-1		1.65 ~ 2.5 mM
3	potassium phosphate		20 mM
4	sodium azide		0.01 %
5	D2O		10.0 ~ 100.0 %

Sample #2

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
6	ZSPA-1	[U-13C; U-15N]	1.5 ~ 2.0 mM
7	Z-domain		1.65 ~ 2.5 mM
8	potassium phosphate		20 mM
9	sodium azide		0.01 %
10	D2O		10.0 ~ 100.0 %

5 HNCO

Instrument

#1 Model Bruker AVANCE (500 MHz)

#2 Model Bruker AVANCE (600 MHz)

#3 Model Varian INOVA (800 MHz)

Sample #1

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
1	Z-domain	[U-13C; U-15N]	1.5 ~ 2.0 mM
2	ZSPA-1		1.65 ~ 2.5 mM
3	potassium phosphate		20 mM
4	sodium azide		0.01 %
5	D2O		10.0 ~ 100.0 %

Sample #2

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
6	ZSPA-1	[U-13C; U-15N]	1.5 ~ 2.0 mM
7	Z-domain		1.65 ~ 2.5 mM
8	potassium phosphate		20 mM
9	sodium azide		0.01 %
10	D2O		10.0 ~ 100.0 %

6 HN(CA)CO

Instrument

#1 Model Bruker AVANCE (500 MHz)

#2 Model Bruker AVANCE (600 MHz)

#3 Model Varian INOVA (800 MHz)

Sample #1

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
1	Z-domain	[U-13C; U-15N]	1.5 ~ 2.0 mM
2	ZSPA-1		1.65 ~ 2.5 mM
3	potassium phosphate		20 mM
4	sodium azide		0.01 %
5	D2O		10.0 ~ 100.0 %

Sample #2

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
6	ZSPA-1	[U-13C; U-15N]	1.5 ~ 2.0 mM
7	Z-domain		1.65 ~ 2.5 mM
8	potassium phosphate		20 mM
9	sodium azide		0.01 %
10	D2O		10.0 ~ 100.0 %

7 HCCH-TOCSY

Instrument

#1 Model Bruker AVANCE (500 MHz)

#2 Model Bruker AVANCE (600 MHz)

#3 Model Varian INOVA (800 MHz)

Sample #1

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
1	Z-domain	[U-13C; U-15N]	1.5 ~ 2.0 mM
2	ZSPA-1		1.65 ~ 2.5 mM
3	potassium phosphate		20 mM
4	sodium azide		0.01 %
5	D2O		10.0 ~ 100.0 %

Sample #2

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
6	ZSPA-1	[U-13C; U-15N]	1.5 ~ 2.0 mM
7	Z-domain		1.65 ~ 2.5 mM
8	potassium phosphate		20 mM
9	sodium azide		0.01 %
10	D2O		10.0 ~ 100.0 %

8 HCCH-COSY

Instrument

#1 Model Bruker AVANCE (500 MHz)

#2 Model Bruker AVANCE (600 MHz)

#3 Model Varian INOVA (800 MHz)

Sample #1

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
1	Z-domain	[U-13C; U-15N]	1.5 ~ 2.0 mM
2	ZSPA-1		1.65 ~ 2.5 mM
3	potassium phosphate		20 mM
4	sodium azide		0.01 %
5	D2O		10.0 ~ 100.0 %

Sample #2

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
6	ZSPA-1	[U-13C; U-15N]	1.5 ~ 2.0 mM
7	Z-domain		1.65 ~ 2.5 mM
8	potassium phosphate		20 mM
9	sodium azide		0.01 %
10	D2O		10.0 ~ 100.0 %

9 15N-TOCSY-HSQC

Instrument

#1 Model Bruker AVANCE (500 MHz)

#2 Model Bruker AVANCE (600 MHz)

#3 Model Varian INOVA (800 MHz)

Sample #1

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
1	Z-domain	[U-13C; U-15N]	1.5 ~ 2.0 mM
2	ZSPA-1		1.65 ~ 2.5 mM
3	potassium phosphate		20 mM
4	sodium azide		0.01 %
5	D2O		10.0 ~ 100.0 %

Sample #2

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
6	ZSPA-1	[U-13C; U-15N]	1.5 ~ 2.0 mM
7	Z-domain		1.65 ~ 2.5 mM
8	potassium phosphate		20 mM
9	sodium azide		0.01 %
10	D2O		10.0 ~ 100.0 %

10 15N-NOESY-HSQC

Instrument

#1 Model Bruker AVANCE (500 MHz)

#2 Model Bruker AVANCE (600 MHz)

#3 Model Varian INOVA (800 MHz)

Sample #1

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
1	Z-domain	[U-13C; U-15N]	1.5 ~ 2.0 mM
2	ZSPA-1		1.65 ~ 2.5 mM
3	potassium phosphate		20 mM
4	sodium azide		0.01 %
5	D2O		10.0 ~ 100.0 %

Sample #2

Temperature 303 (±0.1) K

#	Name	Isotope labeling	Concentration
6	ZSPA-1	[U-13C; U-15N]	1.5 ~ 2.0 mM
7	Z-domain		1.65 ~ 2.5 mM
8	potassium phosphate		20 mM
9	sodium azide		0.01 %
10	D2O		10.0 ~ 100.0 %

Chemical shift validation 5 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr5397_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: bmr5397_3.str

#	Content subtype	Saveframe	Status	# of rows	Sequence coverage (%)
1	Assigned chemical shifts	shift_set_Z-domain	Warning	740	100.0 (chain: 1, length: 58)
2	Assigned chemical shifts	shift_set_ZSPA-1	Warning	746	100.0 (chain: 2, length: 58)
1	Chemical shift references	chemical_shift_reference	OK	3	No information

Assigned chemical shifts

Saveframe: shift_set_Z-domain
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 58, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 427
  - ¹³C chemical shifts: 244
  - ¹⁵N chemical shifts: 69
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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_ZSPA-1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 2, Chain length: 58, Sequence coverage: 100.0%
- Total number of assignments
  - ¹⁵N chemical shifts: 65
  - ¹H chemical shifts: 425
  - ¹³C chemical shifts: 256
- Completeness of assignments
  - Entity_assemble_ID: 2
- 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: 2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	374	373	99.7
¹³C chemical shifts	261	244	93.5
¹⁵N chemical shifts	70	69	98.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	113	112	99.1
¹³C chemical shifts	116	115	99.1
¹⁵N chemical shifts	55	54	98.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	261	261	100.0
¹³C chemical shifts	145	129	89.0
¹⁵N chemical shifts	15	15	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	54	54	100.0
¹H chemical shifts	113	113	100.0
¹³C chemical shifts	116	115	99.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	11	11	100.0
¹H chemical shifts	251	248	98.8
¹³C chemical shifts	148	141	95.3

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Found 1 Document (1.381 seconds)

BMRB: 5397

Sample

Sample

Related entities 1. Z-domain, : 2 : 40 : 67 : 67 entities Detail

Related entities 2. ZSPA-1, : 2 : 2 : 2 : 150 entities Detail

Interaction partners 1. Z-domain, : 1 interactors Detail

Experiments performed 10 experiments Detail

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Chemical shift validation 5 contents Detail