Solution NMR Structure of protein yutD from B.subtilis, Northeast Structural Genomics Consortium Target Target SR232
MIGMSEKRGE IMILIQNAEF ELVHNFKDGF NEEAFKARYS DILNKYDYIV GDWGYGQLRL KGFFDDQNQK ATFETKISTL DEYIYEYCNF GCAYFVLKRI RKLEHHHHHH
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | disulfide | sing | 1:CYS88:SG | 1:CYS92:SG |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 74.8 % (1025 of 1370) | 76.2 % (544 of 714) | 75.3 % (403 of 535) | 64.5 % (78 of 121) |
Backbone | 75.5 % (498 of 660) | 74.1 % (169 of 228) | 79.2 % (255 of 322) | 67.3 % (74 of 110) |
Sidechain | 75.1 % (610 of 812) | 77.2 % (375 of 486) | 73.3 % (231 of 315) | 36.4 % (4 of 11) |
Aromatic | 69.1 % (134 of 194) | 85.6 % (83 of 97) | 52.1 % (50 of 96) | 100.0 % (1 of 1) |
Methyl | 96.9 % (93 of 96) | 95.8 % (46 of 48) | 97.9 % (47 of 48) |
1. SR232
MIGMSEKRGE IMILIQNAEF ELVHNFKDGF NEEAFKARYS DILNKYDYIV GDWGYGQLRL KGFFDDQNQK ATFETKISTL DEYIYEYCNF GCAYFVLKRI RKLEHHHHHHSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | SR232 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | DTT | natural abundance | 10 mM | |
3 | Arginine | natural abundance | 50 mM | |
4 | Bis-Tris pH 6.5 | natural abundance | 50 mM | |
5 | DSS | natural abundance | 50 uM | |
6 | NaN3 | natural abundance | 0.02 % | |
7 | H2O | natural abundance | 90 % | |
8 | 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 | 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 |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | SR232 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | DTT | natural abundance | 10 mM | |
3 | Arginine | natural abundance | 50 mM | |
4 | Bis-Tris pH 6.5 | natural abundance | 50 mM | |
5 | DSS | natural abundance | 50 uM | |
6 | NaN3 | natural abundance | 0.02 % | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | SR232 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | DTT | natural abundance | 10 mM | |
3 | Arginine | natural abundance | 50 mM | |
4 | Bis-Tris pH 6.5 | natural abundance | 50 mM | |
5 | DSS | natural abundance | 50 uM | |
6 | NaN3 | natural abundance | 0.02 % | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | SR232 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | DTT | natural abundance | 10 mM | |
3 | Arginine | natural abundance | 50 mM | |
4 | Bis-Tris pH 6.5 | natural abundance | 50 mM | |
5 | DSS | natural abundance | 50 uM | |
6 | NaN3 | natural abundance | 0.02 % | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | SR232 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | DTT | natural abundance | 10 mM | |
3 | Arginine | natural abundance | 50 mM | |
4 | Bis-Tris pH 6.5 | natural abundance | 50 mM | |
5 | DSS | natural abundance | 50 uM | |
6 | NaN3 | natural abundance | 0.02 % | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | SR232 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | DTT | natural abundance | 10 mM | |
3 | Arginine | natural abundance | 50 mM | |
4 | Bis-Tris pH 6.5 | natural abundance | 50 mM | |
5 | DSS | natural abundance | 50 uM | |
6 | NaN3 | natural abundance | 0.02 % | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | SR232 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | DTT | natural abundance | 10 mM | |
3 | Arginine | natural abundance | 50 mM | |
4 | Bis-Tris pH 6.5 | natural abundance | 50 mM | |
5 | DSS | natural abundance | 50 uM | |
6 | NaN3 | natural abundance | 0.02 % | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | SR232 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | DTT | natural abundance | 10 mM | |
3 | Arginine | natural abundance | 50 mM | |
4 | Bis-Tris pH 6.5 | natural abundance | 50 mM | |
5 | DSS | natural abundance | 50 uM | |
6 | NaN3 | natural abundance | 0.02 % | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | SR232 | [U-100% 13C; U-100% 15N] | 1.1 mM | |
2 | DTT | natural abundance | 10 mM | |
3 | Arginine | natural abundance | 50 mM | |
4 | Bis-Tris pH 6.5 | natural abundance | 50 mM | |
5 | DSS | natural abundance | 50 uM | |
6 | NaN3 | natural abundance | 0.02 % | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints | combined_16384_2kl5.nef |
Input source #2: Coordindates | 2kl5.cif |
Diamagnetism of the molecular assembly | True (excluding Oxygen atoms) |
Whether the assembly has a disulfide bond | True (see coordinates for details) |
Whether the assembly has a other bond | None |
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) |
---|---|---|---|---|
A:88:CYS:SG | A:92:CYS:SG | oxidized, CA 53.5, CB 42.0 ppm | oxidized, CA 55.0, CB 47.4 ppm | 2.031 |
Other 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 MIGMSEKRGEIMILIQNAEFELVHNFKDGFNEEAFKARYSDILNKYDYIVGDWGYGQLRLKGFFDDQNQKATFETKISTLDEYIYEYCNFGCAYFVLKRI |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MIGMSEKRGEIMILIQNAEFELVHNFKDGFNEEAFKARYSDILNKYDYIVGDWGYGQLRLKGFFDDQNQKATFETKISTLDEYIYEYCNFGCAYFVLKRI -------110 RKLEHHHHHH |||||||||| RKLEHHHHHH
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 110 | 0 | 0 | 100.0 |
Content subtype: combined_16384_2kl5.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MIGMSEKRGEIMILIQNAEFELVHNFKDGFNEEAFKARYSDILNKYDYIVGDWGYGQLRLKGFFDDQNQKATFETKISTLDEYIYEYCNFGCAYFVLKRI ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||| ||||||||| .........EIMILIQNAEFELVHNFKDGFNEEAFKARYSDILNKYDYIVGDWGYGQLRLKGFFDDQN...TFETKISTLDEYIYEYCNF.CAYFVLKRI --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -------110 RKLEHHHHHH |||| RKLE ----
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 714 | 531 | 74.4 |
13C chemical shifts | 535 | 382 | 71.4 |
15N chemical shifts | 126 | 72 | 57.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 228 | 161 | 70.6 |
13C chemical shifts | 220 | 158 | 71.8 |
15N chemical shifts | 110 | 68 | 61.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 486 | 370 | 76.1 |
13C chemical shifts | 315 | 224 | 71.1 |
15N chemical shifts | 16 | 4 | 25.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 51 | 46 | 90.2 |
13C chemical shifts | 51 | 46 | 90.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 97 | 82 | 84.5 |
13C chemical shifts | 96 | 47 | 49.0 |
15N chemical shifts | 1 | 1 | 100.0 |
Covalent bonds
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MIGMSEKRGEIMILIQNAEFELVHNFKDGFNEEAFKARYSDILNKYDYIVGDWGYGQLRLKGFFDDQNQKATFETKISTLDEYIYEYCNFGCAYFVLKRI |||||||||||||||||||||||||||||||||||||||||||||| |||||||||||| ||||||||||||||||| | ||||||||| .........EIMILIQNAEFELVHNFKDGFNEEAFKARYSDILNKYDYIVGDWGY.QLRLKGFFDDQN...TFETKISTLDEYIYEYC.F.CAYFVLKRI --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -------110 RKLEHHHHHH || ..LE ----