Solution NMR Structure of YdbC:dT19G1 complex. Northeast Structural Genomics Consortium (NESG) Target KR150
Polymer type: polypeptide(L) polydeoxyribonucleotide
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 89.4 % (939 of 1050) | 87.6 % (543 of 620) | 93.2 % (327 of 351) | 87.3 % (69 of 79) |
Backbone | 87.9 % (473 of 538) | 83.9 % (209 of 249) | 92.2 % (200 of 217) | 88.9 % (64 of 72) |
Sidechain | 91.9 % (534 of 581) | 90.0 % (334 of 371) | 96.1 % (195 of 203) | 71.4 % (5 of 7) |
Aromatic | 85.4 % (82 of 96) | 77.4 % (48 of 62) | 100.0 % (31 of 31) | 100.0 % (3 of 3) |
Methyl | 100.0 % (92 of 92) | 100.0 % (53 of 53) | 100.0 % (39 of 39) |
1. entity 1
MADKLKFEII EELIVLSENA KGWRKELNRV SWNDAEPKYD IRTWSPDHEK MGKGITLSEE EFGVLLKELG NKLE2. DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
TTTTTTTTTT TTTTSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.6 mM KR150.020, 0.6mM dT19G1 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | KR150.020 | [U-100% 13C; U-100% 15N] | 0.6 mM | |
2 | NaN3 | natural abundance | 0.02 % | |
3 | DTT | natural abundance | 10 mM | |
4 | NaCL | natural abundance | 100 mM | |
5 | D2O | natural abundance | 10 % | |
6 | DSS | natural abundance | 50 uM | |
7 | TRIS-HCl | natural abundance | 10 mM | |
8 | DNA chain | natural abundance | 0.3 mM | |
9 | H2O | natural abundance | 90 % |
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 - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.6 mM KR150.020, 0.6mM dT19G1 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | KR150.020 | [U-100% 13C; U-100% 15N] | 0.6 mM | |
2 | NaN3 | natural abundance | 0.02 % | |
3 | DTT | natural abundance | 10 mM | |
4 | NaCL | natural abundance | 100 mM | |
5 | D2O | natural abundance | 10 % | |
6 | DSS | natural abundance | 50 uM | |
7 | TRIS-HCl | natural abundance | 10 mM | |
8 | DNA chain | natural abundance | 0.3 mM | |
9 | H2O | natural abundance | 90 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.6 mM KR150.020, 0.6mM dT19G1 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | KR150.020 | [U-100% 13C; U-100% 15N] | 0.6 mM | |
2 | NaN3 | natural abundance | 0.02 % | |
3 | DTT | natural abundance | 10 mM | |
4 | NaCL | natural abundance | 100 mM | |
5 | D2O | natural abundance | 10 % | |
6 | DSS | natural abundance | 50 uM | |
7 | TRIS-HCl | natural abundance | 10 mM | |
8 | DNA chain | natural abundance | 0.3 mM | |
9 | H2O | natural abundance | 90 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.6 mM KR150.020, 0.6mM dT19G1 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | KR150.020 | [U-100% 13C; U-100% 15N] | 0.6 mM | |
2 | NaN3 | natural abundance | 0.02 % | |
3 | DTT | natural abundance | 10 mM | |
4 | NaCL | natural abundance | 100 mM | |
5 | D2O | natural abundance | 10 % | |
6 | DSS | natural abundance | 50 uM | |
7 | TRIS-HCl | natural abundance | 10 mM | |
8 | DNA chain | natural abundance | 0.3 mM | |
9 | H2O | natural abundance | 90 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.6 mM KR150.020, 0.6mM dT19G1 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | KR150.020 | [U-100% 13C; U-100% 15N] | 0.6 mM | |
2 | NaN3 | natural abundance | 0.02 % | |
3 | DTT | natural abundance | 10 mM | |
4 | NaCL | natural abundance | 100 mM | |
5 | D2O | natural abundance | 10 % | |
6 | DSS | natural abundance | 50 uM | |
7 | TRIS-HCl | natural abundance | 10 mM | |
8 | DNA chain | natural abundance | 0.3 mM | |
9 | H2O | natural abundance | 90 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.6 mM KR150.020, 0.6mM dT19G1 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | KR150.020 | [U-100% 13C; U-100% 15N] | 0.6 mM | |
2 | NaN3 | natural abundance | 0.02 % | |
3 | DTT | natural abundance | 10 mM | |
4 | NaCL | natural abundance | 100 mM | |
5 | D2O | natural abundance | 10 % | |
6 | DSS | natural abundance | 50 uM | |
7 | TRIS-HCl | natural abundance | 10 mM | |
8 | DNA chain | natural abundance | 0.3 mM | |
9 | H2O | natural abundance | 90 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.6 mM KR150.020, 0.6mM dT19G1 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | KR150.020 | [U-100% 13C; U-100% 15N] | 0.6 mM | |
2 | NaN3 | natural abundance | 0.02 % | |
3 | DTT | natural abundance | 10 mM | |
4 | NaCL | natural abundance | 100 mM | |
5 | D2O | natural abundance | 10 % | |
6 | DSS | natural abundance | 50 uM | |
7 | TRIS-HCl | natural abundance | 10 mM | |
8 | DNA chain | natural abundance | 0.3 mM | |
9 | H2O | natural abundance | 90 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.6 mM KR150.020, 0.6mM dT19G1 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | KR150.020 | [U-100% 13C; U-100% 15N] | 0.6 mM | |
2 | NaN3 | natural abundance | 0.02 % | |
3 | DTT | natural abundance | 10 mM | |
4 | NaCL | natural abundance | 100 mM | |
5 | D2O | natural abundance | 10 % | |
6 | DSS | natural abundance | 50 uM | |
7 | TRIS-HCl | natural abundance | 10 mM | |
8 | DNA chain | natural abundance | 0.3 mM | |
9 | H2O | natural abundance | 90 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.6 mM KR150.020, 0.6mM dT19G1 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | KR150.020 | [U-100% 13C; U-100% 15N] | 0.6 mM | |
2 | NaN3 | natural abundance | 0.02 % | |
3 | DTT | natural abundance | 10 mM | |
4 | NaCL | natural abundance | 100 mM | |
5 | D2O | natural abundance | 10 % | |
6 | DSS | natural abundance | 50 uM | |
7 | TRIS-HCl | natural abundance | 10 mM | |
8 | DNA chain | natural abundance | 0.3 mM | |
9 | H2O | natural abundance | 90 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.6 mM KR150.020, 0.6mM dT19G1 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | KR150.020 | [U-100% 13C; U-100% 15N] | 0.6 mM | |
2 | NaN3 | natural abundance | 0.02 % | |
3 | DTT | natural abundance | 10 mM | |
4 | NaCL | natural abundance | 100 mM | |
5 | D2O | natural abundance | 10 % | |
6 | DSS | natural abundance | 50 uM | |
7 | TRIS-HCl | natural abundance | 10 mM | |
8 | DNA chain | natural abundance | 0.3 mM | |
9 | H2O | natural abundance | 90 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.6 mM KR150.020, 0.6mM dT19G1 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | KR150.020 | [U-100% 13C; U-100% 15N] | 0.6 mM | |
2 | NaN3 | natural abundance | 0.02 % | |
3 | DTT | natural abundance | 10 mM | |
4 | NaCL | natural abundance | 100 mM | |
5 | D2O | natural abundance | 10 % | |
6 | DSS | natural abundance | 50 uM | |
7 | TRIS-HCl | natural abundance | 10 mM | |
8 | DNA chain | natural abundance | 0.3 mM | |
9 | H2O | natural abundance | 90 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.6 mM KR150.020, 0.6mM dT19G1 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | KR150.020 | [U-100% 13C; U-100% 15N] | 0.6 mM | |
2 | NaN3 | natural abundance | 0.02 % | |
3 | DTT | natural abundance | 10 mM | |
4 | NaCL | natural abundance | 100 mM | |
5 | D2O | natural abundance | 10 % | |
6 | DSS | natural abundance | 50 uM | |
7 | TRIS-HCl | natural abundance | 10 mM | |
8 | DNA chain | natural abundance | 0.3 mM | |
9 | H2O | natural abundance | 90 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.6 mM KR150.020, 0.6mM dT19G1 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | KR150.020 | [U-100% 13C; U-100% 15N] | 0.6 mM | |
2 | NaN3 | natural abundance | 0.02 % | |
3 | DTT | natural abundance | 10 mM | |
4 | NaCL | natural abundance | 100 mM | |
5 | D2O | natural abundance | 10 % | |
6 | DSS | natural abundance | 50 uM | |
7 | TRIS-HCl | natural abundance | 10 mM | |
8 | DNA chain | natural abundance | 0.3 mM | |
9 | H2O | natural abundance | 90 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.6 mM KR150.020, 0.6mM dT19G1 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | KR150.020 | [U-100% 13C; U-100% 15N] | 0.6 mM | |
2 | NaN3 | natural abundance | 0.02 % | |
3 | DTT | natural abundance | 10 mM | |
4 | NaCL | natural abundance | 100 mM | |
5 | D2O | natural abundance | 10 % | |
6 | DSS | natural abundance | 50 uM | |
7 | TRIS-HCl | natural abundance | 10 mM | |
8 | DNA chain | natural abundance | 0.3 mM | |
9 | H2O | natural abundance | 90 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_18496_2ltt.nef |
Input source #2: Coordindates | 2ltt.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 | None |
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)
NoneNon-standard residues
NoneSequence alignments
--------10--------20--------30--------40--------50--------60--------70--------80 MADKLKFEIIEELIVLSENAKGWRKELNRVSWNDAEPKYDIRTWSPDHEKMGKGITLSEEEFGVLLKELGNKLEHHHHHH |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MADKLKFEIIEELIVLSENAKGWRKELNRVSWNDAEPKYDIRTWSPDHEKMGKGITLSEEEFGVLLKELGNKLEHHHHHH
--------10--------20--------30--------40--------50--------60--------70--------80 MADKLKFEIIEELIVLSENAKGWRKELNRVSWNDAEPKYDIRTWSPDHEKMGKGITLSEEEFGVLLKELGNKLEHHHHHH |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MADKLKFEIIEELIVLSENAKGWRKELNRVSWNDAEPKYDIRTWSPDHEKMGKGITLSEEEFGVLLKELGNKLEHHHHHH
--------10------- TTTTTTTTTTTTTTTTT ||||||||||||||||| TTTTTTTTTTTTTTTTT
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 80 | 0 | 0 | 100.0 |
B | B | 80 | 0 | 0 | 100.0 |
C | C | 17 | 0 | 0 | 100.0 |
Content subtype: combined_18496_2ltt.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80 MADKLKFEIIEELIVLSENAKGWRKELNRVSWNDAEPKYDIRTWSPDHEKMGKGITLSEEEFGVLLKELGNKLEHHHHHH ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| .ADKLKFEIIEELIVLSENAKGWRKELNRVSWNDAEPKYDIRTWSPDHEKMGKGITLSEEEFGVLLKELGNKLE --------10--------20--------30--------40--------50--------60--------70----
--------10------- TTTTTTTTTTTTTTTTT ||||||| ||||||| TTTTTTT...TTTTTTT
Comp_index_ID | Comp_ID | Atom_ID | CS value (ppm) |
---|---|---|---|
24 | ARG | CZ | 159.7 |
29 | ARG | CZ | 159.6 |
32 | TRP | CE2 | 139.9 |
44 | TRP | CE2 | 138.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 516 | 449 | 87.0 |
13C chemical shifts | 381 | 326 | 85.6 |
15N chemical shifts | 88 | 70 | 79.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 163 | 141 | 86.5 |
13C chemical shifts | 160 | 131 | 81.9 |
15N chemical shifts | 78 | 63 | 80.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 353 | 308 | 87.3 |
13C chemical shifts | 221 | 195 | 88.2 |
15N chemical shifts | 10 | 7 | 70.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 41 | 40 | 97.6 |
13C chemical shifts | 41 | 40 | 97.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 46 | 34 | 73.9 |
13C chemical shifts | 43 | 31 | 72.1 |
15N chemical shifts | 3 | 3 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 170 | 98 | 57.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 119 | 70 | 58.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 51 | 28 | 54.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 17 | 14 | 82.4 |
13C chemical shifts | 17 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80 MADKLKFEIIEELIVLSENAKGWRKELNRVSWNDAEPKYDIRTWSPDHEKMGKGITLSEEEFGVLLKELGNKLEHHHHHH |||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||| .ADKLKFEIIEELIVLSENAKGWRKELNRVSWNDAEPKYDIRT.SPDHEKMGKGITLSEEEFGVLLKELGNKLE --------10--------20--------30--------40--------50--------60--------70----
--------10--------20--------30--------40--------50--------60--------70--------80 MADKLKFEIIEELIVLSENAKGWRKELNRVSWNDAEPKYDIRTWSPDHEKMGKGITLSEEEFGVLLKELGNKLEHHHHHH |||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||| .ADKLKFEIIEELIVLSENAKGWRKELNRVSWNDAEPKYDIRT.SPDHEKMGKGITLSEEEFGVLLKELGNKLE --------10--------20--------30--------40--------50--------60--------70----
--------10------- TTTTTTTTTTTTTTTTT ||||||| ||||||| TTTTTTT...TTTTTTT
Dihedral angle restraints
--------10--------20--------30--------40--------50--------60--------70--------80 MADKLKFEIIEELIVLSENAKGWRKELNRVSWNDAEPKYDIRTWSPDHEKMGKGITLSEEEFGVLLKELGNKLEHHHHHH ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MADKLKFEIIEELIVLSENAKGWRKELNRVSWNDAEPKYDIRTWSPDHEKMGKGITLSEEEFGVLLKELGNKLEH --------10--------20--------30--------40--------50--------60--------70-----
--------10--------20--------30--------40--------50--------60--------70--------80 MADKLKFEIIEELIVLSENAKGWRKELNRVSWNDAEPKYDIRTWSPDHEKMGKGITLSEEEFGVLLKELGNKLEHHHHHH ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MADKLKFEIIEELIVLSENAKGWRKELNRVSWNDAEPKYDIRTWSPDHEKMGKGITLSEEEFGVLLKELGNKLEH --------10--------20--------30--------40--------50--------60--------70-----