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BMRB: 19043

2M5A

Protein A binding by an engineered Affibody molecule

Authors

Assembly

Protein A binding by an engineered Affibody molecule

Entity

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

VDNKFNKEQQ NAFYEILHLP NLNEEQRNAF IQSLKDDPSQ SANLLAEAKK LNDAQAPK

2. ZpA963 (polymer, Thiol state: not present), 58 monomers, 6388.022 Da Detail

VDNKFNKETQ EASWEIFTLP NLNGRQVAAF ISSLLDDPSQ SANLLAEAKK LNDAQAPK

Total weight

13028.273 Da

Max. entity weight

6640.251 Da

Source organism

Staphylococcus aureus

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.0 %, Completeness (bb): 97.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.0 % (1339 of 1380)	96.1 % (699 of 727)	97.9 % (507 of 518)	98.5 % (133 of 135)
Backbone	97.1 % (664 of 684)	95.6 % (217 of 227)	97.7 % (339 of 347)	98.2 % (108 of 110)
Sidechain	97.3 % (789 of 811)	96.4 % (482 of 500)	98.6 % (282 of 286)	100.0 % (25 of 25)
Aromatic	95.2 % (80 of 84)	95.2 % (40 of 42)	95.1 % (39 of 41)	100.0 % (1 of 1)
Methyl	98.3 % (116 of 118)	96.6 % (57 of 59)	100.0 % (59 of 59)

1. Z domain

VDNKFNKEQQ NAFYEILHLP NLNEEQRNAF IQSLKDDPSQ SANLLAEAKK LNDAQAPK

2. ZpA963

VDNKFNKETQ EASWEIFTLP NLNGRQVAAF ISSLLDDPSQ SANLLAEAKK LNDAQAPK

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
1	Z domain	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	ZpA963	natural abundance		0.625 ~ 1.25 mM
3	NaCl	natural abundance		75 mM
4	sodium phosphate	natural abundance		20 mM
5	azide	natural abundance		0.1 %

Sample #2

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
6	ZpA963	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
7	Z domain	natural abundance		0.625 ~ 1.25 mM
8	NaCl	natural abundance		75 mM
9	sodium phosphate	natural abundance		20 mM
10	azide	natural abundance		0.1 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2M5A, Strand ID: A, B Detail

Release date

2013-08-13

Citation

High-affinity binding to staphylococcal protein A by an engineered dimeric Affibody molecule
Lindborg, M., Dubnovitsky, A., Olesen, K., Bjorkman, T., Abrahmsen, L., Feldwisch, J., Hard, T.
Protein Eng. Des. Sel. (2013), 26, 635-644, PubMed 23924760 , DOI 10.1093/protein/gzt038 , Abstract

Related entities 1. Z domain, : 2 : 40 : 68 : 66 entities Detail

Related entities 2. ZpA963, : 2 : 2 : 154 entities Detail

Interaction partners 1. Z domain, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 30 experiments Detail

1 3D HNCO

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
1	Z domain	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	ZpA963	natural abundance		0.625 ~ 1.25 mM
3	NaCl	natural abundance		75 mM
4	sodium phosphate	natural abundance		20 mM
5	azide	natural abundance		0.1 %

2 3D HNCA

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
1	Z domain	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	ZpA963	natural abundance		0.625 ~ 1.25 mM
3	NaCl	natural abundance		75 mM
4	sodium phosphate	natural abundance		20 mM
5	azide	natural abundance		0.1 %

3 3D HN(CO)CA

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
1	Z domain	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	ZpA963	natural abundance		0.625 ~ 1.25 mM
3	NaCl	natural abundance		75 mM
4	sodium phosphate	natural abundance		20 mM
5	azide	natural abundance		0.1 %

4 3D HNCACB

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
1	Z domain	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	ZpA963	natural abundance		0.625 ~ 1.25 mM
3	NaCl	natural abundance		75 mM
4	sodium phosphate	natural abundance		20 mM
5	azide	natural abundance		0.1 %

5 3D HN(CO)CACB

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
1	Z domain	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	ZpA963	natural abundance		0.625 ~ 1.25 mM
3	NaCl	natural abundance		75 mM
4	sodium phosphate	natural abundance		20 mM
5	azide	natural abundance		0.1 %

6 3D 1H-15N TOCSY

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
1	Z domain	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	ZpA963	natural abundance		0.625 ~ 1.25 mM
3	NaCl	natural abundance		75 mM
4	sodium phosphate	natural abundance		20 mM
5	azide	natural abundance		0.1 %

7 3D HCCH-COSY

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
1	Z domain	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	ZpA963	natural abundance		0.625 ~ 1.25 mM
3	NaCl	natural abundance		75 mM
4	sodium phosphate	natural abundance		20 mM
5	azide	natural abundance		0.1 %

8 3D HCCH-TOCSY

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
1	Z domain	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	ZpA963	natural abundance		0.625 ~ 1.25 mM
3	NaCl	natural abundance		75 mM
4	sodium phosphate	natural abundance		20 mM
5	azide	natural abundance		0.1 %

9 2D 1H-15N HSQC

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
1	Z domain	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	ZpA963	natural abundance		0.625 ~ 1.25 mM
3	NaCl	natural abundance		75 mM
4	sodium phosphate	natural abundance		20 mM
5	azide	natural abundance		0.1 %

10 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
1	Z domain	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	ZpA963	natural abundance		0.625 ~ 1.25 mM
3	NaCl	natural abundance		75 mM
4	sodium phosphate	natural abundance		20 mM
5	azide	natural abundance		0.1 %

11 2D (HB)CB(CGCDCE)HE

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
1	Z domain	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	ZpA963	natural abundance		0.625 ~ 1.25 mM
3	NaCl	natural abundance		75 mM
4	sodium phosphate	natural abundance		20 mM
5	azide	natural abundance		0.1 %

12 3D 1H-15N NOESY

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
1	Z domain	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	ZpA963	natural abundance		0.625 ~ 1.25 mM
3	NaCl	natural abundance		75 mM
4	sodium phosphate	natural abundance		20 mM
5	azide	natural abundance		0.1 %

13 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
1	Z domain	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	ZpA963	natural abundance		0.625 ~ 1.25 mM
3	NaCl	natural abundance		75 mM
4	sodium phosphate	natural abundance		20 mM
5	azide	natural abundance		0.1 %

14 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
1	Z domain	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	ZpA963	natural abundance		0.625 ~ 1.25 mM
3	NaCl	natural abundance		75 mM
4	sodium phosphate	natural abundance		20 mM
5	azide	natural abundance		0.1 %

15 2D F1(13C,15N)-filtered, F2(13C)-edited NOESY

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
1	Z domain	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	ZpA963	natural abundance		0.625 ~ 1.25 mM
3	NaCl	natural abundance		75 mM
4	sodium phosphate	natural abundance		20 mM
5	azide	natural abundance		0.1 %

16 3D HNCO

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
6	ZpA963	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
7	Z domain	natural abundance		0.625 ~ 1.25 mM
8	NaCl	natural abundance		75 mM
9	sodium phosphate	natural abundance		20 mM
10	azide	natural abundance		0.1 %

17 3D HNCA

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
6	ZpA963	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
7	Z domain	natural abundance		0.625 ~ 1.25 mM
8	NaCl	natural abundance		75 mM
9	sodium phosphate	natural abundance		20 mM
10	azide	natural abundance		0.1 %

18 3D HN(CO)CA

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
6	ZpA963	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
7	Z domain	natural abundance		0.625 ~ 1.25 mM
8	NaCl	natural abundance		75 mM
9	sodium phosphate	natural abundance		20 mM
10	azide	natural abundance		0.1 %

19 3D HNCACB

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
6	ZpA963	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
7	Z domain	natural abundance		0.625 ~ 1.25 mM
8	NaCl	natural abundance		75 mM
9	sodium phosphate	natural abundance		20 mM
10	azide	natural abundance		0.1 %

20 3D HN(CO)CACB

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
6	ZpA963	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
7	Z domain	natural abundance		0.625 ~ 1.25 mM
8	NaCl	natural abundance		75 mM
9	sodium phosphate	natural abundance		20 mM
10	azide	natural abundance		0.1 %

21 3D 1H-15N TOCSY

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
6	ZpA963	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
7	Z domain	natural abundance		0.625 ~ 1.25 mM
8	NaCl	natural abundance		75 mM
9	sodium phosphate	natural abundance		20 mM
10	azide	natural abundance		0.1 %

22 3D HCCH-COSY

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
6	ZpA963	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
7	Z domain	natural abundance		0.625 ~ 1.25 mM
8	NaCl	natural abundance		75 mM
9	sodium phosphate	natural abundance		20 mM
10	azide	natural abundance		0.1 %

23 3D HCCH-TOCSY

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
6	ZpA963	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
7	Z domain	natural abundance		0.625 ~ 1.25 mM
8	NaCl	natural abundance		75 mM
9	sodium phosphate	natural abundance		20 mM
10	azide	natural abundance		0.1 %

24 2D 1H-15N HSQC

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
6	ZpA963	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
7	Z domain	natural abundance		0.625 ~ 1.25 mM
8	NaCl	natural abundance		75 mM
9	sodium phosphate	natural abundance		20 mM
10	azide	natural abundance		0.1 %

25 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
6	ZpA963	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
7	Z domain	natural abundance		0.625 ~ 1.25 mM
8	NaCl	natural abundance		75 mM
9	sodium phosphate	natural abundance		20 mM
10	azide	natural abundance		0.1 %

26 2D (HB)CB(CGCDCE)HE

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
6	ZpA963	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
7	Z domain	natural abundance		0.625 ~ 1.25 mM
8	NaCl	natural abundance		75 mM
9	sodium phosphate	natural abundance		20 mM
10	azide	natural abundance		0.1 %

27 3D 1H-15N NOESY

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
6	ZpA963	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
7	Z domain	natural abundance		0.625 ~ 1.25 mM
8	NaCl	natural abundance		75 mM
9	sodium phosphate	natural abundance		20 mM
10	azide	natural abundance		0.1 %

28 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
6	ZpA963	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
7	Z domain	natural abundance		0.625 ~ 1.25 mM
8	NaCl	natural abundance		75 mM
9	sodium phosphate	natural abundance		20 mM
10	azide	natural abundance		0.1 %

29 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
6	ZpA963	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
7	Z domain	natural abundance		0.625 ~ 1.25 mM
8	NaCl	natural abundance		75 mM
9	sodium phosphate	natural abundance		20 mM
10	azide	natural abundance		0.1 %

30 2D F1(13C,15N)-filtered, F2(13C)-edited NOESY

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 5.6, Details 13C,15N labeled Z domain with 25% molar excess ZpA963

#	Name	Isotope labeling	Type	Concentration
6	ZpA963	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
7	Z domain	natural abundance		0.625 ~ 1.25 mM
8	NaCl	natural abundance		75 mM
9	sodium phosphate	natural abundance		20 mM
10	azide	natural abundance		0.1 %

nullKeywords Affibody molecule, binding protein, protein A, protein engineering, Z domain