Solution structure of DnaK suppressor protein from Agrobacterium tumefaciens C58. Northeast Structural Genomics Consortium target AtT12/Ontario Center for Structural Proteomics Target atc0888
LAGGKSMNVE SYEKILRDRQ RELYRRLHKI EADFEEPRNP DDEDRASERS NDEVLDELGQ VGQDELRAID AALARIASGT FGTCVKCGKR ISEDRLKAVP YTPFCQECAA AL
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 95.2 % (1206 of 1267) | 95.8 % (639 of 667) | 94.2 % (457 of 485) | 95.7 % (110 of 115) |
Backbone | 95.8 % (636 of 664) | 95.2 % (216 of 227) | 96.4 % (317 of 329) | 95.4 % (103 of 108) |
Sidechain | 95.3 % (675 of 708) | 96.1 % (423 of 440) | 93.9 % (245 of 261) | 100.0 % (7 of 7) |
Aromatic | 63.8 % (37 of 58) | 82.8 % (24 of 29) | 44.8 % (13 of 29) | |
Methyl | 100.0 % (110 of 110) | 100.0 % (55 of 55) | 100.0 % (55 of 55) |
1. atc0888
LAGGKSMNVE SYEKILRDRQ RELYRRLHKI EADFEEPRNP DDEDRASERS NDEVLDELGQ VGQDELRAID AALARIASGT FGTCVKCGKR ISEDRLKAVP YTPFCQECAA ALSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | atc0888 | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | benzamidine | natural abundance | 10 mM | |
7 | inhibitor cocktail | natural abundance | 1 na | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
10 | atc0888 | [U-7% 13C; U-100% 15N] | 0.5 mM | |
11 | TRIS | [U-100% 2H] | 10 mM | |
12 | sodium chloride | natural abundance | 300 mM | |
13 | zinc sulphate | natural abundance | 10 uM | |
14 | DTT | [U-100% 2H] | 10 mM | |
15 | benzamidine | natural abundance | 10 mM | |
16 | inhibitor cocktail | natural abundance | 1 na | |
17 | H2O | natural abundance | 90 % | |
18 | D2O | natural abundance | 10 % |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | atc0888 | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | benzamidine | natural abundance | 10 mM | |
7 | inhibitor cocktail | natural abundance | 1 na | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | atc0888 | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | benzamidine | natural abundance | 10 mM | |
7 | inhibitor cocktail | natural abundance | 1 na | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | atc0888 | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | benzamidine | natural abundance | 10 mM | |
7 | inhibitor cocktail | natural abundance | 1 na | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | atc0888 | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | benzamidine | natural abundance | 10 mM | |
7 | inhibitor cocktail | natural abundance | 1 na | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | atc0888 | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | benzamidine | natural abundance | 10 mM | |
7 | inhibitor cocktail | natural abundance | 1 na | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | atc0888 | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | benzamidine | natural abundance | 10 mM | |
7 | inhibitor cocktail | natural abundance | 1 na | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | atc0888 | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | benzamidine | natural abundance | 10 mM | |
7 | inhibitor cocktail | natural abundance | 1 na | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | atc0888 | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | benzamidine | natural abundance | 10 mM | |
7 | inhibitor cocktail | natural abundance | 1 na | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | atc0888 | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | benzamidine | natural abundance | 10 mM | |
7 | inhibitor cocktail | natural abundance | 1 na | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | atc0888 | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | benzamidine | natural abundance | 10 mM | |
7 | inhibitor cocktail | natural abundance | 1 na | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | atc0888 | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | benzamidine | natural abundance | 10 mM | |
7 | inhibitor cocktail | natural abundance | 1 na | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
10 | atc0888 | [U-7% 13C; U-100% 15N] | 0.5 mM | |
11 | TRIS | [U-100% 2H] | 10 mM | |
12 | sodium chloride | natural abundance | 300 mM | |
13 | zinc sulphate | natural abundance | 10 uM | |
14 | DTT | [U-100% 2H] | 10 mM | |
15 | benzamidine | natural abundance | 10 mM | |
16 | inhibitor cocktail | natural abundance | 1 na | |
17 | H2O | natural abundance | 90 % | |
18 | D2O | natural abundance | 10 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_16594_2kq9.nef |
Input source #2: Coordindates | 2kq9.cif |
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
NoneOther 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) |
---|---|---|---|---|
1:84:CYS:SG | 2:1:ZN:ZN | unknown | unknown | n/a |
1:87:CYS:SG | 2:1:ZN:ZN | unknown | unknown | n/a |
1:105:CYS:SG | 2:1:ZN:ZN | unknown | unknown | n/a |
1:108:CYS:SG | 2:1:ZN:ZN | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 1 | ZN | ZINC ION | None |
Sequence alignments
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 LAGGKSMNVESYEKILRDRQRELYRRLHKIEADFEEPRNPDDEDRASERSNDEVLDELGQVGQDELRAIDAALARIASGTFGTCVKCGKRISEDRLKAVP |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| LAGGKSMNVESYEKILRDRQRELYRRLHKIEADFEEPRNPDDEDRASERSNDEVLDELGQVGQDELRAIDAALARIASGTFGTCVKCGKRISEDRLKAVP -------110-- YTPFCQECAAAL |||||||||||| YTPFCQECAAAL
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 112 | 0 | 0 | 100.0 |
Content subtype: combined_16594_2kq9.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 LAGGKSMNVESYEKILRDRQRELYRRLHKIEADFEEPRNPDDEDRASERSNDEVLDELGQVGQDELRAIDAALARIASGTFGTCVKCGKRISEDRLKAVP ||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| LAG.KSMNVESYEKILRDRQRELYRRLHKIEADFEEPRNPDDEDRASERSNDEVLDELGQVGQDELRAIDAALARIASGTFGTCVKCGKRISEDRLKAVP -------110-- YTPFCQECAAAL |||||||||||| YTPFCQECAAAL
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 667 | 640 | 96.0 |
13C chemical shifts | 485 | 457 | 94.2 |
15N chemical shifts | 127 | 110 | 86.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 227 | 217 | 95.6 |
13C chemical shifts | 224 | 212 | 94.6 |
15N chemical shifts | 108 | 103 | 95.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 440 | 423 | 96.1 |
13C chemical shifts | 261 | 245 | 93.9 |
15N chemical shifts | 19 | 7 | 36.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 56 | 56 | 100.0 |
13C chemical shifts | 56 | 56 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 29 | 24 | 82.8 |
13C chemical shifts | 29 | 13 | 44.8 |
Covalent bonds
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 LAGGKSMNVESYEKILRDRQRELYRRLHKIEADFEEPRNPDDEDRASERSNDEVLDELGQVGQDELRAIDAALARIASGTFGTCVKCGKRISEDRLKAVP || |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| LA..KSMNVESYEKILRDRQRELYRRLHKIEADFEEPRNPDDEDRASERSNDEVLDELGQVGQDELRAIDAALARIASGTFGTCVKCGKRISEDRLKAVP -------110-- YTPFCQECAAAL |||||||||||| YTPFCQECAAAL
Dihedral angle restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 LAGGKSMNVESYEKILRDRQRELYRRLHKIEADFEEPRNPDDEDRASERSNDEVLDELGQVGQDELRAIDAALARIASGTFGTCVKCGKRISEDRLKAVP ||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| .......NVESYEKILRDRQRELYRRLH...........................DELGQVGQDELRAIDAALARIASGTFGTCVKCGKRISEDRLKAV. --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -------110-- YTPFCQECAAAL ||||||||||| YTPFCQECAAA -------110-