SOLUTION STRUCTURE OF THE S. AUREUS SORTASE A-SUBSTRATE COMPLEX
MQAKPQIPKD KSKVAGYIEI PDADIKEPVY PGPATPEQLN RGVSFAEENE SLDDQNISIA GHTFIDRPNY QFTNLKAAKK GSMVYFKVGN ETRKYKMTSI RDVKPTDVGV LDEQKGKDKQ LTLITCDDYN EKTGVWEKRK IFVATEVK
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | disulfide | sing | 1:CYS126:SG | 2:B275:SG |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 91.8 % (1648 of 1796) | 90.8 % (859 of 946) | 91.5 % (635 of 694) | 98.7 % (154 of 156) |
Backbone | 97.7 % (866 of 886) | 99.3 % (299 of 301) | 96.2 % (427 of 444) | 99.3 % (140 of 141) |
Sidechain | 87.5 % (921 of 1052) | 86.8 % (560 of 645) | 88.5 % (347 of 392) | 93.3 % (14 of 15) |
Aromatic | 45.6 % (52 of 114) | 45.6 % (26 of 57) | 44.6 % (25 of 56) | 100.0 % (1 of 1) |
Methyl | 100.0 % (152 of 152) | 100.0 % (76 of 76) | 100.0 % (76 of 76) |
1. Sortase A
MQAKPQIPKD KSKVAGYIEI PDADIKEPVY PGPATPEQLN RGVSFAEENE SLDDQNISIA GHTFIDRPNY QFTNLKAAKK GSMVYFKVGN ETRKYKMTSI RDVKPTDVGV LDEQKGKDKQ LTLITCDDYN EKTGVWEKRK IFVATEVK2. Cbz-LPAT
XLPAXSolvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 302 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Sortase A | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | Cbz-LPAT* | natural abundance | 1 mM | |
3 | TRIS | natural abundance | 50 mM | |
4 | sodium chloride | natural abundance | 100 mM | |
5 | Calcium Chloride | natural abundance | 20 mM | |
6 | sodium azide | natural abundance | 0.01 % | |
7 | H2O | natural abundance | 93 % | |
8 | D2O | [U-100% 2H] | 7 % |
Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 302 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
9 | Sortase A | [U-100% 15N] | 1 mM | |
10 | Cbz-LPAT* | natural abundance | 1 mM | |
11 | TRIS | natural abundance | 50 mM | |
12 | sodium chloride | natural abundance | 100 mM | |
13 | Calcium Chloride | natural abundance | 20 mM | |
14 | sodium azide | natural abundance | 0.01 % | |
15 | H2O | natural abundance | 93 % | |
16 | D2O | [U-100% 2H] | 7 % |
Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 302 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
17 | Sortase A | [U-100% 13C; U-100% 15N] | 1 mM | |
18 | Cbz-LPAT* | natural abundance | 1 mM | |
19 | TRIS | natural abundance | 50 mM | |
20 | sodium chloride | natural abundance | 100 mM | |
21 | Calcium Chloride | natural abundance | 20 mM | |
22 | sodium azide | natural abundance | 0.01 % | |
23 | H2O | natural abundance | 93 % | |
24 | D2O | [U-100% 2H] | 7 % |
Bruker AVANCE - 500 MHz
State isotropic, Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 302 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
9 | Sortase A | [U-100% 15N] | 1 mM | |
10 | Cbz-LPAT* | natural abundance | 1 mM | |
11 | TRIS | natural abundance | 50 mM | |
12 | sodium chloride | natural abundance | 100 mM | |
13 | Calcium Chloride | natural abundance | 20 mM | |
14 | sodium azide | natural abundance | 0.01 % | |
15 | H2O | natural abundance | 93 % | |
16 | D2O | [U-100% 2H] | 7 % |
Bruker AVANCE - 500 MHz
State isotropic, Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 302 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
17 | Sortase A | [U-100% 13C; U-100% 15N] | 1 mM | |
18 | Cbz-LPAT* | natural abundance | 1 mM | |
19 | TRIS | natural abundance | 50 mM | |
20 | sodium chloride | natural abundance | 100 mM | |
21 | Calcium Chloride | natural abundance | 20 mM | |
22 | sodium azide | natural abundance | 0.01 % | |
23 | H2O | natural abundance | 93 % | |
24 | D2O | [U-100% 2H] | 7 % |
Bruker AVANCE - 500 MHz
State isotropic, Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 302 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Sortase A | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | Cbz-LPAT* | natural abundance | 1 mM | |
3 | TRIS | natural abundance | 50 mM | |
4 | sodium chloride | natural abundance | 100 mM | |
5 | Calcium Chloride | natural abundance | 20 mM | |
6 | sodium azide | natural abundance | 0.01 % | |
7 | H2O | natural abundance | 93 % | |
8 | D2O | [U-100% 2H] | 7 % |
Bruker AVANCE - 500 MHz
State isotropic, Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 302 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Sortase A | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | Cbz-LPAT* | natural abundance | 1 mM | |
3 | TRIS | natural abundance | 50 mM | |
4 | sodium chloride | natural abundance | 100 mM | |
5 | Calcium Chloride | natural abundance | 20 mM | |
6 | sodium azide | natural abundance | 0.01 % | |
7 | H2O | natural abundance | 93 % | |
8 | D2O | [U-100% 2H] | 7 % |
Bruker AVANCE - 500 MHz
State isotropic, Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 302 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
17 | Sortase A | [U-100% 13C; U-100% 15N] | 1 mM | |
18 | Cbz-LPAT* | natural abundance | 1 mM | |
19 | TRIS | natural abundance | 50 mM | |
20 | sodium chloride | natural abundance | 100 mM | |
21 | Calcium Chloride | natural abundance | 20 mM | |
22 | sodium azide | natural abundance | 0.01 % | |
23 | H2O | natural abundance | 93 % | |
24 | D2O | [U-100% 2H] | 7 % |
Bruker AVANCE - 500 MHz
State isotropic, Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 302 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
17 | Sortase A | [U-100% 13C; U-100% 15N] | 1 mM | |
18 | Cbz-LPAT* | natural abundance | 1 mM | |
19 | TRIS | natural abundance | 50 mM | |
20 | sodium chloride | natural abundance | 100 mM | |
21 | Calcium Chloride | natural abundance | 20 mM | |
22 | sodium azide | natural abundance | 0.01 % | |
23 | H2O | natural abundance | 93 % | |
24 | D2O | [U-100% 2H] | 7 % |
Bruker AVANCE - 500 MHz
State isotropic, Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 302 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
17 | Sortase A | [U-100% 13C; U-100% 15N] | 1 mM | |
18 | Cbz-LPAT* | natural abundance | 1 mM | |
19 | TRIS | natural abundance | 50 mM | |
20 | sodium chloride | natural abundance | 100 mM | |
21 | Calcium Chloride | natural abundance | 20 mM | |
22 | sodium azide | natural abundance | 0.01 % | |
23 | H2O | natural abundance | 93 % | |
24 | D2O | [U-100% 2H] | 7 % |
Bruker AVANCE - 500 MHz
State isotropic, Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 302 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
17 | Sortase A | [U-100% 13C; U-100% 15N] | 1 mM | |
18 | Cbz-LPAT* | natural abundance | 1 mM | |
19 | TRIS | natural abundance | 50 mM | |
20 | sodium chloride | natural abundance | 100 mM | |
21 | Calcium Chloride | natural abundance | 20 mM | |
22 | sodium azide | natural abundance | 0.01 % | |
23 | H2O | natural abundance | 93 % | |
24 | D2O | [U-100% 2H] | 7 % |
Bruker AVANCE - 500 MHz
State isotropic, Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 302 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
17 | Sortase A | [U-100% 13C; U-100% 15N] | 1 mM | |
18 | Cbz-LPAT* | natural abundance | 1 mM | |
19 | TRIS | natural abundance | 50 mM | |
20 | sodium chloride | natural abundance | 100 mM | |
21 | Calcium Chloride | natural abundance | 20 mM | |
22 | sodium azide | natural abundance | 0.01 % | |
23 | H2O | natural abundance | 93 % | |
24 | D2O | [U-100% 2H] | 7 % |
Bruker AVANCE - 500 MHz
State isotropic, Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 302 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
17 | Sortase A | [U-100% 13C; U-100% 15N] | 1 mM | |
18 | Cbz-LPAT* | natural abundance | 1 mM | |
19 | TRIS | natural abundance | 50 mM | |
20 | sodium chloride | natural abundance | 100 mM | |
21 | Calcium Chloride | natural abundance | 20 mM | |
22 | sodium azide | natural abundance | 0.01 % | |
23 | H2O | natural abundance | 93 % | |
24 | D2O | [U-100% 2H] | 7 % |
Bruker AVANCE - 500 MHz
State isotropic, Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 302 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
17 | Sortase A | [U-100% 13C; U-100% 15N] | 1 mM | |
18 | Cbz-LPAT* | natural abundance | 1 mM | |
19 | TRIS | natural abundance | 50 mM | |
20 | sodium chloride | natural abundance | 100 mM | |
21 | Calcium Chloride | natural abundance | 20 mM | |
22 | sodium azide | natural abundance | 0.01 % | |
23 | H2O | natural abundance | 93 % | |
24 | D2O | [U-100% 2H] | 7 % |
Bruker AVANCE - 500 MHz
State isotropic, Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 302 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
17 | Sortase A | [U-100% 13C; U-100% 15N] | 1 mM | |
18 | Cbz-LPAT* | natural abundance | 1 mM | |
19 | TRIS | natural abundance | 50 mM | |
20 | sodium chloride | natural abundance | 100 mM | |
21 | Calcium Chloride | natural abundance | 20 mM | |
22 | sodium azide | natural abundance | 0.01 % | |
23 | H2O | natural abundance | 93 % | |
24 | D2O | [U-100% 2H] | 7 % |
Bruker AVANCE - 500 MHz
State isotropic, Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 302 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
17 | Sortase A | [U-100% 13C; U-100% 15N] | 1 mM | |
18 | Cbz-LPAT* | natural abundance | 1 mM | |
19 | TRIS | natural abundance | 50 mM | |
20 | sodium chloride | natural abundance | 100 mM | |
21 | Calcium Chloride | natural abundance | 20 mM | |
22 | sodium azide | natural abundance | 0.01 % | |
23 | H2O | natural abundance | 93 % | |
24 | D2O | [U-100% 2H] | 7 % |
Bruker AVANCE - 500 MHz
State isotropic, Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 302 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
17 | Sortase A | [U-100% 13C; U-100% 15N] | 1 mM | |
18 | Cbz-LPAT* | natural abundance | 1 mM | |
19 | TRIS | natural abundance | 50 mM | |
20 | sodium chloride | natural abundance | 100 mM | |
21 | Calcium Chloride | natural abundance | 20 mM | |
22 | sodium azide | natural abundance | 0.01 % | |
23 | H2O | natural abundance | 93 % | |
24 | D2O | [U-100% 2H] | 7 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints | combined_16270_2kid.nef |
Input source #2: Coordindates | 2kid.cif |
Diamagnetism of the molecular assembly | False (excluding Oxygen atoms) |
Whether the assembly has a disulfide bond | True (see coordinates for details) |
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
Ptnr_site_1 | Ptnr_site_2 | Redox_state_prediction_1 | Redox_state_prediction_2 | Distance (Å) |
---|---|---|---|---|
2:5:B27:SG | 1:126:CYS:SG | unknown | unknown | n/a |
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) |
---|---|---|---|---|
2:1:PHQ:C1 | 2:2:LEU:N | unknown | unknown | n/a |
2:4:ALA:C | 2:5:B27:N | unknown | unknown | n/a |
1:50:GLU:OE2 | 3:1:CA:CA | unknown | unknown | n/a |
1:56:ASN:O | 3:1:CA:CA | unknown | unknown | n/a |
1:113:GLU:OE1 | 3:1:CA:CA | unknown | unknown | n/a |
1:47:GLU:OE2 | 3:1:CA:CA | unknown | unknown | n/a |
1:54:ASP:OD2 | 3:1:CA:CA | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 1 | CA | CALCIUM ION | Distance restraints |
C | 701 | PHQ | benzyl chlorocarbonate | Coordinates |
C | 705 | B27 | (2R,3S) 3-amino-4-mercapto-2-butanol | Assigned chemical shifts, Distance restraints, Coordinates |
Sequence alignments
-60-------70--------80--------90-------100-------110-------120-------130-------140-------150-------1 MQAKPQIPKDKSKVAGYIEIPDADIKEPVYPGPATPEQLNRGVSFAEENESLDDQNISIAGHTFIDRPNYQFTNLKAAKKGSMVYFKVGNETRKYKMTSI |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MQAKPQIPKDKSKVAGYIEIPDADIKEPVYPGPATPEQLNRGVSFAEENESLDDQNISIAGHTFIDRPNYQFTNLKAAKKGSMVYFKVGNETRKYKMTSI --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 60-------170-------180-------190-------200------ RDVKPTDVGVLDEQKGKDKQLTLITCDDYNEKTGVWEKRKIFVATEVK |||||||||||||||||||||||||||||||||||||||||||||||| RDVKPTDVGVLDEQKGKDKQLTLITCDDYNEKTGVWEKRKIFVATEVK -------110-------120-------130-------140--------
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 148 | 0 | 0 | 100.0 |
C | C | 5 | 0 | 0 | 100.0 |
Content subtype: combined_16270_2kid.nef
Assigned chemical shifts
-60-------70--------80--------90-------100-------110-------120-------130-------140-------150-------1 MQAKPQIPKDKSKVAGYIEIPDADIKEPVYPGPATPEQLNRGVSFAEENESLDDQNISIAGHTFIDRPNYQFTNLKAAKKGSMVYFKVGNETRKYKMTSI |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MQAKPQIPKDKSKVAGYIEIPDADIKEPVYPGPATPEQLNRGVSFAEENESLDDQNISIAGHTFIDRPNYQFTNLKAAKKGSMVYFKVGNETRKYKMTSI 60-------170-------180-------190-------200------ RDVKPTDVGVLDEQKGKDKQLTLITCDDYNEKTGVWEKRKIFVATEVK |||||||||||||||||||||||||||||||||||||||||||||||| RDVKPTDVGVLDEQKGKDKQLTLITCDDYNEKTGVWEKRKIFVATEVK
----- XLPAX |||| .LPAX
Comp_index_ID | Comp_ID | Atom_ID | CS value (ppm) |
---|---|---|---|
131 | THR | HG1 | 6.45 |
180 | THR | HG1 | 7.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 929 | 836 | 90.0 |
13C chemical shifts | 680 | 621 | 91.3 |
15N chemical shifts | 159 | 154 | 96.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 296 | 293 | 99.0 |
13C chemical shifts | 296 | 282 | 95.3 |
15N chemical shifts | 139 | 137 | 98.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 633 | 543 | 85.8 |
13C chemical shifts | 384 | 339 | 88.3 |
15N chemical shifts | 20 | 17 | 85.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 76 | 76 | 100.0 |
13C chemical shifts | 76 | 76 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 57 | 26 | 45.6 |
13C chemical shifts | 56 | 25 | 44.6 |
15N chemical shifts | 1 | 1 | 100.0 |
Comp_index_ID | Comp_ID |
---|---|
701 | PHQ |
705 | B27 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 17 | 15 | 88.2 |
13C chemical shifts | 14 | 12 | 85.7 |
15N chemical shifts | 2 | 2 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 5 | 5 | 100.0 |
13C chemical shifts | 6 | 4 | 66.7 |
15N chemical shifts | 2 | 2 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 12 | 10 | 83.3 |
13C chemical shifts | 8 | 8 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 3 | 3 | 100.0 |
13C chemical shifts | 3 | 3 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
Covalent bonds
Distance restraints
-60-------70--------80--------90-------100-------110-------120-------130-------140-------150-------1 MQAKPQIPKDKSKVAGYIEIPDADIKEPVYPGPATPEQLNRGVSFAEENESLDDQNISIAGHTFIDRPNYQFTNLKAAKKGSMVYFKVGNETRKYKMTSI ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| .QAKPQIPKDKSKVAGYIEIPDADIKEPVYPGPATPEQLNRGVSFAEENESLDDQNISIAGHTFIDRPNYQFTNLKAAKKGSMVYFKVGNETRKYKMTSI 60-------170-------180-------190-------200------ RDVKPTDVGVLDEQKGKDKQLTLITCDDYNEKTGVWEKRKIFVATEVK |||||||||||||||||||||||||||||||||||||||||||||||| RDVKPTDVGVLDEQKGKDKQLTLITCDDYNEKTGVWEKRKIFVATEVK
Dihedral angle restraints
-60-------70--------80--------90-------100-------110-------120-------130-------140-------150-------1 MQAKPQIPKDKSKVAGYIEIPDADIKEPVYPGPATPEQLNRGVSFAEENESLDDQNISIAGHTFIDRPNYQFTNLKAAKKGSMVYFKVGNETRKYKMTSI |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||| MQAKPQIPKDKSKVAGYIEIPDADIKEPVYPGPATPEQLNRGVS.AEENESLDDQNISIAGHTFIDRPNYQFTNLKAAKKGSMVYFKVGNETRKYKMTSI 60-------170-------180-------190-------200------ RDVKPTDVGVLDEQKGKDKQLTLITCDDYNEKTGVWEKRKIFVATEVK |||||||||||||||||||||||||||||||||||||||||||||||| RDVKPTDVGVLDEQKGKDKQLTLITCDDYNEKTGVWEKRKIFVATEVK
----- XLPAX ||| .LPA ----
RDC restraints
-60-------70--------80--------90-------100-------110-------120-------130-------140-------150-------1 MQAKPQIPKDKSKVAGYIEIPDADIKEPVYPGPATPEQLNRGVSFAEENESLDDQNISIAGHTFIDRPNYQFTNLKAAKKGSMVYFKVGNETRKYKMTSI |||| |||| ||||| ||||||| ||||| ||| ||| || || || || ||||||||| |||||||||| ||||| ..AKPQ...DKSK.AGYIE.PDADIKE...PGPAT...LNR.......NES.DD.NI..AG...ID......TNLKAAKKG..VYFKVGNETR..KMTSI 60-------170-------180-------190-------200------ RDVKPTDVGVLDEQKGKDKQLTLITCDDYNEKTGVWEKRKIFVATEVK | || ||| || ||||||| || |||||| || |||| R.VK.TDV.VL..QKGKDKQ.TL.....YNEKTG.......FV.TEVK