Solution NMR Structure of the folded C-terminal fragment of YiaD from Escherichia coli, Northeast Structural Genomics Consortium Target ER553.
YYMDVQEAKL RDKMRGTGVS VTRSGDNIIL NMPNNVTFDS SSATLKPAGA NTLTGVAMVL KEYPKTAVNV IGYTDSTGGH DLNMRLSQQR ADSVASALIT QGVDASRIRT QGLGPANPIA SNSTAEGKAQ NRRVEITLSP LLEHHHHHH
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 95.9 % (1564 of 1631) | 96.4 % (811 of 841) | 95.1 % (600 of 631) | 96.2 % (153 of 159) |
Backbone | 96.7 % (853 of 882) | 97.4 % (296 of 304) | 96.1 % (418 of 435) | 97.2 % (139 of 143) |
Sidechain | 93.7 % (830 of 886) | 94.0 % (505 of 537) | 93.4 % (311 of 333) | 87.5 % (14 of 16) |
Aromatic | 57.1 % (40 of 70) | 60.0 % (21 of 35) | 54.3 % (19 of 35) | |
Methyl | 100.0 % (174 of 174) | 100.0 % (87 of 87) | 100.0 % (87 of 87) |
1. YiaD
YYMDVQEAKL RDKMRGTGVS VTRSGDNIIL NMPNNVTFDS SSATLKPAGA NTLTGVAMVL KEYPKTAVNV IGYTDSTGGH DLNMRLSQQR ADSVASALIT QGVDASRIRT QGLGPANPIA SNSTAEGKAQ NRRVEITLSP LLEHHHHHHSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-100% 13C; U-100% 15N] | 1.9 (±0.1) mM | |
2 | MES | natural abundance | 20 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±5.0) mM | |
4 | calcium chloride | natural abundance | 5 (±0.2) mM | |
5 | DTT | natural abundance | 10 (±0.5) mM | |
6 | sodium azide | natural abundance | 0.02 (±0.001) % |
Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | entity | [U-5% 13C; U-100% 15N] | 1.3 (±0.1) mM | |
8 | MES | natural abundance | 20 (±1.0) mM | |
9 | sodium chloride | natural abundance | 100 (±5.0) mM | |
10 | calcium chloride | natural abundance | 5 (±0.2) mM | |
11 | DTT | natural abundance | 10 (±0.5) mM | |
12 | sodium azide | natural abundance | 0.02 (±0.001) % |
Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
13 | entity | [U-100% 13C; U-100% 15N] | 1.9 (±0.1) mM | |
14 | MES | natural abundance | 20 (±1.0) mM | |
15 | sodium chloride | natural abundance | 100 (±5.0) mM | |
16 | calcium chloride | natural abundance | 5 (±0.2) mM | |
17 | DTT | natural abundance | 10 (±0.5) mM | |
18 | sodium azide | natural abundance | 0.02 (±0.001) % |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | null | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | null | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | null | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | null | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | null | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | null | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | null | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | null | indirect | 0.1013291 |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-100% 13C; U-100% 15N] | 1.9 (±0.1) mM | |
2 | MES | natural abundance | 20 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±5.0) mM | |
4 | calcium chloride | natural abundance | 5 (±0.2) mM | |
5 | DTT | natural abundance | 10 (±0.5) mM | |
6 | sodium azide | natural abundance | 0.02 (±0.001) % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-100% 13C; U-100% 15N] | 1.9 (±0.1) mM | |
2 | MES | natural abundance | 20 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±5.0) mM | |
4 | calcium chloride | natural abundance | 5 (±0.2) mM | |
5 | DTT | natural abundance | 10 (±0.5) mM | |
6 | sodium azide | natural abundance | 0.02 (±0.001) % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | entity | [U-5% 13C; U-100% 15N] | 1.3 (±0.1) mM | |
8 | MES | natural abundance | 20 (±1.0) mM | |
9 | sodium chloride | natural abundance | 100 (±5.0) mM | |
10 | calcium chloride | natural abundance | 5 (±0.2) mM | |
11 | DTT | natural abundance | 10 (±0.5) mM | |
12 | sodium azide | natural abundance | 0.02 (±0.001) % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-100% 13C; U-100% 15N] | 1.9 (±0.1) mM | |
2 | MES | natural abundance | 20 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±5.0) mM | |
4 | calcium chloride | natural abundance | 5 (±0.2) mM | |
5 | DTT | natural abundance | 10 (±0.5) mM | |
6 | sodium azide | natural abundance | 0.02 (±0.001) % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-100% 13C; U-100% 15N] | 1.9 (±0.1) mM | |
2 | MES | natural abundance | 20 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±5.0) mM | |
4 | calcium chloride | natural abundance | 5 (±0.2) mM | |
5 | DTT | natural abundance | 10 (±0.5) mM | |
6 | sodium azide | natural abundance | 0.02 (±0.001) % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
13 | entity | [U-100% 13C; U-100% 15N] | 1.9 (±0.1) mM | |
14 | MES | natural abundance | 20 (±1.0) mM | |
15 | sodium chloride | natural abundance | 100 (±5.0) mM | |
16 | calcium chloride | natural abundance | 5 (±0.2) mM | |
17 | DTT | natural abundance | 10 (±0.5) mM | |
18 | sodium azide | natural abundance | 0.02 (±0.001) % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-100% 13C; U-100% 15N] | 1.9 (±0.1) mM | |
2 | MES | natural abundance | 20 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±5.0) mM | |
4 | calcium chloride | natural abundance | 5 (±0.2) mM | |
5 | DTT | natural abundance | 10 (±0.5) mM | |
6 | sodium azide | natural abundance | 0.02 (±0.001) % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-100% 13C; U-100% 15N] | 1.9 (±0.1) mM | |
2 | MES | natural abundance | 20 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±5.0) mM | |
4 | calcium chloride | natural abundance | 5 (±0.2) mM | |
5 | DTT | natural abundance | 10 (±0.5) mM | |
6 | sodium azide | natural abundance | 0.02 (±0.001) % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-100% 13C; U-100% 15N] | 1.9 (±0.1) mM | |
2 | MES | natural abundance | 20 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±5.0) mM | |
4 | calcium chloride | natural abundance | 5 (±0.2) mM | |
5 | DTT | natural abundance | 10 (±0.5) mM | |
6 | sodium azide | natural abundance | 0.02 (±0.001) % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-100% 13C; U-100% 15N] | 1.9 (±0.1) mM | |
2 | MES | natural abundance | 20 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±5.0) mM | |
4 | calcium chloride | natural abundance | 5 (±0.2) mM | |
5 | DTT | natural abundance | 10 (±0.5) mM | |
6 | sodium azide | natural abundance | 0.02 (±0.001) % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-100% 13C; U-100% 15N] | 1.9 (±0.1) mM | |
2 | MES | natural abundance | 20 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±5.0) mM | |
4 | calcium chloride | natural abundance | 5 (±0.2) mM | |
5 | DTT | natural abundance | 10 (±0.5) mM | |
6 | sodium azide | natural abundance | 0.02 (±0.001) % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-100% 13C; U-100% 15N] | 1.9 (±0.1) mM | |
2 | MES | natural abundance | 20 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±5.0) mM | |
4 | calcium chloride | natural abundance | 5 (±0.2) mM | |
5 | DTT | natural abundance | 10 (±0.5) mM | |
6 | sodium azide | natural abundance | 0.02 (±0.001) % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-100% 13C; U-100% 15N] | 1.9 (±0.1) mM | |
2 | MES | natural abundance | 20 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±5.0) mM | |
4 | calcium chloride | natural abundance | 5 (±0.2) mM | |
5 | DTT | natural abundance | 10 (±0.5) mM | |
6 | sodium azide | natural abundance | 0.02 (±0.001) % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-100% 13C; U-100% 15N] | 1.9 (±0.1) mM | |
2 | MES | natural abundance | 20 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±5.0) mM | |
4 | calcium chloride | natural abundance | 5 (±0.2) mM | |
5 | DTT | natural abundance | 10 (±0.5) mM | |
6 | sodium azide | natural abundance | 0.02 (±0.001) % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-100% 13C; U-100% 15N] | 1.9 (±0.1) mM | |
2 | MES | natural abundance | 20 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±5.0) mM | |
4 | calcium chloride | natural abundance | 5 (±0.2) mM | |
5 | DTT | natural abundance | 10 (±0.5) mM | |
6 | sodium azide | natural abundance | 0.02 (±0.001) % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-100% 13C; U-100% 15N] | 1.9 (±0.1) mM | |
2 | MES | natural abundance | 20 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±5.0) mM | |
4 | calcium chloride | natural abundance | 5 (±0.2) mM | |
5 | DTT | natural abundance | 10 (±0.5) mM | |
6 | sodium azide | natural abundance | 0.02 (±0.001) % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
13 | entity | [U-100% 13C; U-100% 15N] | 1.9 (±0.1) mM | |
14 | MES | natural abundance | 20 (±1.0) mM | |
15 | sodium chloride | natural abundance | 100 (±5.0) mM | |
16 | calcium chloride | natural abundance | 5 (±0.2) mM | |
17 | DTT | natural abundance | 10 (±0.5) mM | |
18 | sodium azide | natural abundance | 0.02 (±0.001) % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-100% 13C; U-100% 15N] | 1.9 (±0.1) mM | |
2 | MES | natural abundance | 20 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±5.0) mM | |
4 | calcium chloride | natural abundance | 5 (±0.2) mM | |
5 | DTT | natural abundance | 10 (±0.5) mM | |
6 | sodium azide | natural abundance | 0.02 (±0.001) % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_15683_2k1s.nef |
Input source #2: Coordindates | 2k1s.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--------90-------100 YYMDVQEAKLRDKMRGTGVSVTRSGDNIILNMPNNVTFDSSSATLKPAGANTLTGVAMVLKEYPKTAVNVIGYTDSTGGHDLNMRLSQQRADSVASALIT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| YYMDVQEAKLRDKMRGTGVSVTRSGDNIILNMPNNVTFDSSSATLKPAGANTLTGVAMVLKEYPKTAVNVIGYTDSTGGHDLNMRLSQQRADSVASALIT -------110-------120-------130-------140--------- QGVDASRIRTQGLGPANPIASNSTAEGKAQNRRVEITLSPLLEHHHHHH ||||||||||||||||||||||||||||||||||||||||||||||||| QGVDASRIRTQGLGPANPIASNSTAEGKAQNRRVEITLSPLLEHHHHHH
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 149 | 0 | 0 | 100.0 |
Content subtype: combined_15683_2k1s.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 YYMDVQEAKLRDKMRGTGVSVTRSGDNIILNMPNNVTFDSSSATLKPAGANTLTGVAMVLKEYPKTAVNVIGYTDSTGGHDLNMRLSQQRADSVASALIT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| YYMDVQEAKLRDKMRGTGVSVTRSGDNIILNMPNNVTFDSSSATLKPAGANTLTGVAMVLKEYPKTAVNVIGYTDSTGGHDLNMRLSQQRADSVASALIT --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -------110-------120-------130-------140--------- QGVDASRIRTQGLGPANPIASNSTAEGKAQNRRVEITLSPLLEHHHHHH |||||||||||||||||||||||||||||||||||||||||||||| QGVDASRIRTQGLGPANPIASNSTAEGKAQNRRVEITLSPLLEHHH -------110-------120-------130-------140------
Comp_index_ID | Comp_ID | Atom_ID | CS value (ppm) |
---|---|---|---|
17 | THR | HG1 | 6.01 |
52 | THR | HG1 | 5.52 |
54 | THR | HG1 | 5.26 |
66 | THR | HG1 | 6.36 |
124 | THR | HG1 | 5.69 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 841 | 809 | 96.2 |
13C chemical shifts | 631 | 596 | 94.5 |
15N chemical shifts | 168 | 161 | 95.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 304 | 296 | 97.4 |
13C chemical shifts | 298 | 282 | 94.6 |
15N chemical shifts | 143 | 138 | 96.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 537 | 513 | 95.5 |
13C chemical shifts | 333 | 314 | 94.3 |
15N chemical shifts | 25 | 23 | 92.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 92 | 92 | 100.0 |
13C chemical shifts | 92 | 92 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 35 | 21 | 60.0 |
13C chemical shifts | 35 | 19 | 54.3 |
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 YYMDVQEAKLRDKMRGTGVSVTRSGDNIILNMPNNVTFDSSSATLKPAGANTLTGVAMVLKEYPKTAVNVIGYTDSTGGHDLNMRLSQQRADSVASALIT ||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| YYMDVQEAKLRDKMRGTGVSVTRSGDNIILNMPNNVTFD.SSATLKPAGANTLTGVAMVLKEYPKTAVNVIGYTDSTGGHDLNMRLSQQRADSVASALIT --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -------110-------120-------130-------140--------- QGVDASRIRTQGLGPANPIASNSTAEGKAQNRRVEITLSPLLEHHHHHH |||||||||||||||||||||||||||||||||||||||||||| QGVDASRIRTQGLGPANPIASNSTAEGKAQNRRVEITLSPLLEH -------110-------120-------130-------140----
Dihedral angle restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 YYMDVQEAKLRDKMRGTGVSVTRSGDNIILNMPNNVTFDSSSATLKPAGANTLTGVAMVLKEYPKTAVNVIGYTDSTGGHDLNMRLSQQRADSVASALIT |||||||||||| |||||||| ||||||||||| ||| ||||||||||||||||||||| |||||||||| |||||||||||||||||||||| ..MDVQEAKLRDKM...GVSVTRSG.NIILNMPNNVT.DSS.ATLKPAGANTLTGVAMVLKEY.KTAVNVIGYT....GHDLNMRLSQQRADSVASALIT --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -------110-------120-------130-------140--------- QGVDASRIRTQGLGPANPIASNSTAEGKAQNRRVEITLSPLLEHHHHHH |||||||||||| ||||||||||||||||||||||| QGVDASRIRTQG......IASNSTAEGKAQNRRVEITLSPL -------110-------120-------130-------140-