Structures of the reduced and oxidized state of the mutant D24A of yeast thioredoxin 1: insight into the mechanism for the closing of the water cavity
MVTQFKTASE FDSAIAQDKL VVVAFYATWC GPCKMIAPMI EKFSEQYPQA DFYKLDVDEL GDVAQKNEVS AMPTLLLFKN GKEVAKVVGA NPAAIKQAIA ANA
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 81.1 % (966 of 1191) | 78.8 % (483 of 613) | 81.2 % (381 of 469) | 93.6 % (102 of 109) |
Backbone | 95.4 % (580 of 608) | 94.6 % (194 of 205) | 95.7 % (292 of 305) | 95.9 % (94 of 98) |
Sidechain | 69.6 % (475 of 682) | 69.6 % (284 of 408) | 69.6 % (183 of 263) | 72.7 % (8 of 11) |
Aromatic | 66.7 % (64 of 96) | 66.7 % (32 of 48) | 68.1 % (32 of 47) | 0.0 % (0 of 1) |
Methyl | 75.4 % (95 of 126) | 81.0 % (51 of 63) | 69.8 % (44 of 63) |
1. Yeast Thioredoxin 1 redcuced
MVTQFKTASE FDSAIAQDKL VVVAFYATWC GPCKMIAPMI EKFSEQYPQA DFYKLDVDEL GDVAQKNEVS AMPTLLLFKN GKEVAKVVGA NPAAIKQAIA ANASolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | yTrx1D24A reduced | [U-100% 13C; U-100% 15N] | 850 uM | |
2 | H2O | natural abundance | 90 % | |
3 | 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 NOESY HSCQ (15N), NOESY HSCQ (AROMATIC),
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | yTrx1D24A reduced | [U-100% 13C; U-100% 15N] | 850 uM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz NOESY HSCQ (15N), NOESY HSCQ (AROMATIC),
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | yTrx1D24A reduced | [U-100% 13C; U-100% 15N] | 850 uM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz NOESY HSCQ (15N), NOESY HSCQ (AROMATIC),
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | yTrx1D24A reduced | [U-100% 13C; U-100% 15N] | 850 uM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Bruker Avance - 700 MHz HNCO, CBCACONH, HCCH COSY, HHCH TOCSY, TRHBHACONH, NOESY HSCQ (aliphatic),
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | yTrx1D24A reduced | [U-100% 13C; U-100% 15N] | 850 uM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Bruker Avance - 700 MHz HNCO, CBCACONH, HCCH COSY, HHCH TOCSY, TRHBHACONH, NOESY HSCQ (aliphatic),
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | yTrx1D24A reduced | [U-100% 13C; U-100% 15N] | 850 uM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Bruker Avance - 700 MHz HNCO, CBCACONH, HCCH COSY, HHCH TOCSY, TRHBHACONH, NOESY HSCQ (aliphatic),
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | yTrx1D24A reduced | [U-100% 13C; U-100% 15N] | 850 uM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Bruker Avance - 700 MHz HNCO, CBCACONH, HCCH COSY, HHCH TOCSY, TRHBHACONH, NOESY HSCQ (aliphatic),
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | yTrx1D24A reduced | [U-100% 13C; U-100% 15N] | 850 uM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Bruker Avance - 700 MHz HNCO, CBCACONH, HCCH COSY, HHCH TOCSY, TRHBHACONH, NOESY HSCQ (aliphatic),
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | yTrx1D24A reduced | [U-100% 13C; U-100% 15N] | 850 uM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Bruker Avance - 700 MHz HNCO, CBCACONH, HCCH COSY, HHCH TOCSY, TRHBHACONH, NOESY HSCQ (aliphatic),
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | yTrx1D24A reduced | [U-100% 13C; U-100% 15N] | 850 uM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz NOESY HSCQ (15N), NOESY HSCQ (AROMATIC),
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | yTrx1D24A reduced | [U-100% 13C; U-100% 15N] | 850 uM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Bruker Avance - 700 MHz HNCO, CBCACONH, HCCH COSY, HHCH TOCSY, TRHBHACONH, NOESY HSCQ (aliphatic),
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | yTrx1D24A reduced | [U-100% 13C; U-100% 15N] | 850 uM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz NOESY HSCQ (15N), NOESY HSCQ (AROMATIC),
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | yTrx1D24A reduced | [U-100% 13C; U-100% 15N] | 850 uM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_25702_2n5a.nef |
Input source #2: Coordindates | 2n5a.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 MVTQFKTASEFDSAIAQDKLVVVAFYATWCGPCKMIAPMIEKFSEQYPQADFYKLDVDELGDVAQKNEVSAMPTLLLFKNGKEVAKVVGANPAAIKQAIA |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MVTQFKTASEFDSAIAQDKLVVVAFYATWCGPCKMIAPMIEKFSEQYPQADFYKLDVDELGDVAQKNEVSAMPTLLLFKNGKEVAKVVGANPAAIKQAIA --- ANA ||| ANA
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 103 | 0 | 0 | 100.0 |
Content subtype: combined_25702_2n5a.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MVTQFKTASEFDSAIAQDKLVVVAFYATWCGPCKMIAPMIEKFSEQYPQADFYKLDVDELGDVAQKNEVSAMPTLLLFKNGKEVAKVVGANPAAIKQAIA |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MVTQFKTASEFDSAIAQDKLVVVAFYATWC..CKMIAPMIEKFSEQYPQADFYKLDVDELGDVAQKNEVSAMPTLLLFKNGKEVAKVVGANPAAIKQAIA --- ANA ||| ANA
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 613 | 485 | 79.1 |
13C chemical shifts | 469 | 380 | 81.0 |
15N chemical shifts | 109 | 102 | 93.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 205 | 196 | 95.6 |
13C chemical shifts | 206 | 194 | 94.2 |
15N chemical shifts | 98 | 94 | 95.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 408 | 289 | 70.8 |
13C chemical shifts | 263 | 186 | 70.7 |
15N chemical shifts | 11 | 8 | 72.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 67 | 57 | 85.1 |
13C chemical shifts | 67 | 49 | 73.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 48 | 32 | 66.7 |
13C chemical shifts | 47 | 32 | 68.1 |
15N chemical shifts | 1 | 0 | 0.0 |
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MVTQFKTASEFDSAIAQDKLVVVAFYATWCGPCKMIAPMIEKFSEQYPQADFYKLDVDELGDVAQKNEVSAMPTLLLFKNGKEVAKVVGANPAAIKQAIA |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MVTQFKTASEFDSAIAQDKLVVVAFYATWC..CKMIAPMIEKFSEQYPQADFYKLDVDELGDVAQKNEVSAMPTLLLFKNGKEVAKVVGANPAAIKQAIA --- ANA ||| ANA
Dihedral angle restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MVTQFKTASEFDSAIAQDKLVVVAFYATWCGPCKMIAPMIEKFSEQYPQADFYKLDVDELGDVAQKNEVSAMPTLLLFKNGKEVAKVVGANPAAIKQAIA |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| MVTQFKTASEFDSAIAQDKLVVVAFYATWCGPCKMIAPMIEKFSEQYPQADFYKLDVDELGDVAQKNEVSAMPTLLLFKNGKEVAKVV.ANPAAIKQAIA --- ANA ||| ANA