NMR Structure of Protein YfgJ from Salmonella Typhimurium. Northeast Structural Genomics Target StR86.
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | na | sing | 1:CYS5:SG | 2:ZN1:ZN |
2 | na | sing | 1:CYS8:SG | 2:ZN1:ZN |
3 | na | sing | 1:CYS21:SG | 2:ZN1:ZN |
4 | na | sing | 1:CYS24:SG | 2:ZN1:ZN |
5 | na | sing | 1:CYS34:SG | 2:ZN1:ZN |
6 | na | sing | 1:CYS37:SG | 2:ZN1:ZN |
7 | na | sing | 1:CYS54:SG | 2:ZN1:ZN |
8 | na | sing | 1:HIS58:NE2 | 2:ZN1:ZN |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 91.6 % (838 of 915) | 91.5 % (433 of 473) | 92.7 % (330 of 356) | 87.2 % (75 of 86) |
Backbone | 96.7 % (464 of 480) | 97.5 % (159 of 163) | 96.7 % (231 of 239) | 94.9 % (74 of 78) |
Sidechain | 88.1 % (451 of 512) | 88.4 % (274 of 310) | 90.7 % (176 of 194) | 12.5 % (1 of 8) |
Aromatic | 59.0 % (46 of 78) | 59.0 % (23 of 39) | 59.0 % (23 of 39) | |
Methyl | 100.0 % (78 of 78) | 100.0 % (39 of 39) | 100.0 % (39 of 39) |
1. protein
MEITCPVCHH ALERNGDTAH CETCAKDFSL QALCPDCRQP LQVLKACGAV DYFCQNGHGL ISKKRVNFVI SDQLEHHHHH HSolvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 4.5 (±0.2)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | protein | [U-100% 13C; U-100% 15N] | 1 (±0.2) mM | |
2 | NH4OAc | natural abundance | 20 (±1.0) mM | |
3 | NaCl | natural abundance | 100 (±5.0) mM | |
4 | DTT | natural abundance | 10 (±1.0) mM | |
5 | CaCl2 | natural abundance | 5 (±1.0) mM | |
6 | NaN3 | natural abundance | 0.02 (±0.001) % | |
7 | H2O | 95 % | ||
8 | D2O | 5 % |
Solvent system 100% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 4.5 (±0.2)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
9 | protein | [U-100% 13C; U-100% 15N] | 1 (±0.2) mM | |
10 | NH4OAc | natural abundance | 20 (±1.0) mM | |
11 | NaCl | natural abundance | 100 (±5.0) mM | |
12 | DTT | natural abundance | 10 (±1.0) mM | |
13 | CaCl2 | natural abundance | 5 (±1.0) mM | |
14 | NaN3 | natural abundance | 0.02 (±0.001) % | |
15 | D2O | 100 % |
Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 4.5 (±0.2)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
16 | protein | [U-5% 13C; U-100% 15N] | 1.7 (±0.2) mM | |
17 | NH4OAc | natural abundance | 20 (±1.0) mM | |
18 | NaCl | natural abundance | 100 (±5.0) mM | |
19 | DTT | natural abundance | 10 (±1.0) mM | |
20 | CaCl2 | natural abundance | 5 (±1.0) mM | |
21 | NaN3 | natural abundance | 0.02 (±0.001) % | |
22 | H2O | 95 % | ||
23 | D2O | 5 % |
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 - 750 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 4.5 (±0.2)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | protein | [U-100% 13C; U-100% 15N] | 1 (±0.2) mM | |
2 | NH4OAc | natural abundance | 20 (±1.0) mM | |
3 | NaCl | natural abundance | 100 (±5.0) mM | |
4 | DTT | natural abundance | 10 (±1.0) mM | |
5 | CaCl2 | natural abundance | 5 (±1.0) mM | |
6 | NaN3 | natural abundance | 0.02 (±0.001) % | |
7 | H2O | 95 % | ||
8 | D2O | 5 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 4.5 (±0.2)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | protein | [U-100% 13C; U-100% 15N] | 1 (±0.2) mM | |
2 | NH4OAc | natural abundance | 20 (±1.0) mM | |
3 | NaCl | natural abundance | 100 (±5.0) mM | |
4 | DTT | natural abundance | 10 (±1.0) mM | |
5 | CaCl2 | natural abundance | 5 (±1.0) mM | |
6 | NaN3 | natural abundance | 0.02 (±0.001) % | |
7 | H2O | 95 % | ||
8 | D2O | 5 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 4.5 (±0.2)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
16 | protein | [U-5% 13C; U-100% 15N] | 1.7 (±0.2) mM | |
17 | NH4OAc | natural abundance | 20 (±1.0) mM | |
18 | NaCl | natural abundance | 100 (±5.0) mM | |
19 | DTT | natural abundance | 10 (±1.0) mM | |
20 | CaCl2 | natural abundance | 5 (±1.0) mM | |
21 | NaN3 | natural abundance | 0.02 (±0.001) % | |
22 | H2O | 95 % | ||
23 | D2O | 5 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 4.5 (±0.2)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | protein | [U-100% 13C; U-100% 15N] | 1 (±0.2) mM | |
2 | NH4OAc | natural abundance | 20 (±1.0) mM | |
3 | NaCl | natural abundance | 100 (±5.0) mM | |
4 | DTT | natural abundance | 10 (±1.0) mM | |
5 | CaCl2 | natural abundance | 5 (±1.0) mM | |
6 | NaN3 | natural abundance | 0.02 (±0.001) % | |
7 | H2O | 95 % | ||
8 | D2O | 5 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 4.5 (±0.2)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | protein | [U-100% 13C; U-100% 15N] | 1 (±0.2) mM | |
2 | NH4OAc | natural abundance | 20 (±1.0) mM | |
3 | NaCl | natural abundance | 100 (±5.0) mM | |
4 | DTT | natural abundance | 10 (±1.0) mM | |
5 | CaCl2 | natural abundance | 5 (±1.0) mM | |
6 | NaN3 | natural abundance | 0.02 (±0.001) % | |
7 | H2O | 95 % | ||
8 | D2O | 5 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 4.5 (±0.2)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | protein | [U-100% 13C; U-100% 15N] | 1 (±0.2) mM | |
2 | NH4OAc | natural abundance | 20 (±1.0) mM | |
3 | NaCl | natural abundance | 100 (±5.0) mM | |
4 | DTT | natural abundance | 10 (±1.0) mM | |
5 | CaCl2 | natural abundance | 5 (±1.0) mM | |
6 | NaN3 | natural abundance | 0.02 (±0.001) % | |
7 | H2O | 95 % | ||
8 | D2O | 5 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 4.5 (±0.2)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | protein | [U-100% 13C; U-100% 15N] | 1 (±0.2) mM | |
2 | NH4OAc | natural abundance | 20 (±1.0) mM | |
3 | NaCl | natural abundance | 100 (±5.0) mM | |
4 | DTT | natural abundance | 10 (±1.0) mM | |
5 | CaCl2 | natural abundance | 5 (±1.0) mM | |
6 | NaN3 | natural abundance | 0.02 (±0.001) % | |
7 | H2O | 95 % | ||
8 | D2O | 5 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 4.5 (±0.2)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | protein | [U-100% 13C; U-100% 15N] | 1 (±0.2) mM | |
2 | NH4OAc | natural abundance | 20 (±1.0) mM | |
3 | NaCl | natural abundance | 100 (±5.0) mM | |
4 | DTT | natural abundance | 10 (±1.0) mM | |
5 | CaCl2 | natural abundance | 5 (±1.0) mM | |
6 | NaN3 | natural abundance | 0.02 (±0.001) % | |
7 | H2O | 95 % | ||
8 | D2O | 5 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 4.5 (±0.2)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | protein | [U-100% 13C; U-100% 15N] | 1 (±0.2) mM | |
2 | NH4OAc | natural abundance | 20 (±1.0) mM | |
3 | NaCl | natural abundance | 100 (±5.0) mM | |
4 | DTT | natural abundance | 10 (±1.0) mM | |
5 | CaCl2 | natural abundance | 5 (±1.0) mM | |
6 | NaN3 | natural abundance | 0.02 (±0.001) % | |
7 | H2O | 95 % | ||
8 | D2O | 5 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 4.5 (±0.2)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | protein | [U-100% 13C; U-100% 15N] | 1 (±0.2) mM | |
2 | NH4OAc | natural abundance | 20 (±1.0) mM | |
3 | NaCl | natural abundance | 100 (±5.0) mM | |
4 | DTT | natural abundance | 10 (±1.0) mM | |
5 | CaCl2 | natural abundance | 5 (±1.0) mM | |
6 | NaN3 | natural abundance | 0.02 (±0.001) % | |
7 | H2O | 95 % | ||
8 | D2O | 5 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 4.5 (±0.2)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | protein | [U-100% 13C; U-100% 15N] | 1 (±0.2) mM | |
2 | NH4OAc | natural abundance | 20 (±1.0) mM | |
3 | NaCl | natural abundance | 100 (±5.0) mM | |
4 | DTT | natural abundance | 10 (±1.0) mM | |
5 | CaCl2 | natural abundance | 5 (±1.0) mM | |
6 | NaN3 | natural abundance | 0.02 (±0.001) % | |
7 | H2O | 95 % | ||
8 | D2O | 5 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 4.5 (±0.2)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | protein | [U-100% 13C; U-100% 15N] | 1 (±0.2) mM | |
2 | NH4OAc | natural abundance | 20 (±1.0) mM | |
3 | NaCl | natural abundance | 100 (±5.0) mM | |
4 | DTT | natural abundance | 10 (±1.0) mM | |
5 | CaCl2 | natural abundance | 5 (±1.0) mM | |
6 | NaN3 | natural abundance | 0.02 (±0.001) % | |
7 | H2O | 95 % | ||
8 | D2O | 5 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 4.5 (±0.2)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
9 | protein | [U-100% 13C; U-100% 15N] | 1 (±0.2) mM | |
10 | NH4OAc | natural abundance | 20 (±1.0) mM | |
11 | NaCl | natural abundance | 100 (±5.0) mM | |
12 | DTT | natural abundance | 10 (±1.0) mM | |
13 | CaCl2 | natural abundance | 5 (±1.0) mM | |
14 | NaN3 | natural abundance | 0.02 (±0.001) % | |
15 | D2O | 100 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 4.5 (±0.2)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
9 | protein | [U-100% 13C; U-100% 15N] | 1 (±0.2) mM | |
10 | NH4OAc | natural abundance | 20 (±1.0) mM | |
11 | NaCl | natural abundance | 100 (±5.0) mM | |
12 | DTT | natural abundance | 10 (±1.0) mM | |
13 | CaCl2 | natural abundance | 5 (±1.0) mM | |
14 | NaN3 | natural abundance | 0.02 (±0.001) % | |
15 | D2O | 100 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 4.5 (±0.2)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
9 | protein | [U-100% 13C; U-100% 15N] | 1 (±0.2) mM | |
10 | NH4OAc | natural abundance | 20 (±1.0) mM | |
11 | NaCl | natural abundance | 100 (±5.0) mM | |
12 | DTT | natural abundance | 10 (±1.0) mM | |
13 | CaCl2 | natural abundance | 5 (±1.0) mM | |
14 | NaN3 | natural abundance | 0.02 (±0.001) % | |
15 | D2O | 100 % |
Varian INOVA - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 4.5 (±0.2)
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | protein | [U-100% 13C; U-100% 15N] | 1 (±0.2) mM | |
2 | NH4OAc | natural abundance | 20 (±1.0) mM | |
3 | NaCl | natural abundance | 100 (±5.0) mM | |
4 | DTT | natural abundance | 10 (±1.0) mM | |
5 | CaCl2 | natural abundance | 5 (±1.0) mM | |
6 | NaN3 | natural abundance | 0.02 (±0.001) % | |
7 | H2O | 95 % | ||
8 | D2O | 5 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints | combined_15338_2jrp.nef |
Input source #2: Coordindates | 2jrp.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 | Error |
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) |
---|---|---|---|---|
1:22:GLU:OE1 | 2:1:ZN:ZN | unknown | unknown | n/a |
1:22:GLU:OE2 | 2:1:ZN:ZN | unknown | unknown | n/a |
1:23:THR:O | 2:1:ZN:ZN | unknown | unknown | n/a |
1:23:THR:OG1 | 2:1:ZN:ZN | unknown | unknown | n/a |
1:58:HIS:ND1 | 2:2:ZN:ZN | unknown | unknown | n/a |
1:59:GLY:O | 2:2:ZN:ZN | unknown | unknown | n/a |
1:8:CYS:SG | 2:1:ZN:ZN | unknown | unknown | n/a |
1:54:CYS:SG | 2:2: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 | Distance restraints |
B | 2 | ZN | ZINC ION | None |
Sequence alignments
--------10--------20--------30--------40--------50--------60--------70--------80- MEITCPVCHHALERNGDTAHCETCAKDFSLQALCPDCRQPLQVLKACGAVDYFCQNGHGLISKKRVNFVISDQLEHHHHHH ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MEITCPVCHHALERNGDTAHCETCAKDFSLQALCPDCRQPLQVLKACGAVDYFCQNGHGLISKKRVNFVISDQLEHHHHHH
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 81 | 0 | 0 | 100.0 |
Content subtype: combined_15338_2jrp.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80- MEITCPVCHHALERNGDTAHCETCAKDFSLQALCPDCRQPLQVLKACGAVDYFCQNGHGLISKKRVNFVISDQLEHHHHHH ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MEITCPVCHHALERNGDTAHCETCAKDFSLQALCPDCRQPLQVLKACGAVDYFCQNGHGLISKKRVNFVISDQLEHHHHHH
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 473 | 430 | 90.9 |
13C chemical shifts | 356 | 330 | 92.7 |
15N chemical shifts | 89 | 74 | 83.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 163 | 158 | 96.9 |
13C chemical shifts | 162 | 154 | 95.1 |
15N chemical shifts | 78 | 73 | 93.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 310 | 272 | 87.7 |
13C chemical shifts | 194 | 176 | 90.7 |
15N chemical shifts | 11 | 1 | 9.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 40 | 39 | 97.5 |
13C chemical shifts | 40 | 39 | 97.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 39 | 23 | 59.0 |
13C chemical shifts | 39 | 23 | 59.0 |
Covalent bonds
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80- MEITCPVCHHALERNGDTAHCETCAKDFSLQALCPDCRQPLQVLKACGAVDYFCQNGHGLISKKRVNFVISDQLEHHHHHH ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| .EITCPVCHHALERNGDTAHCETCAKDFSLQALCPDCRQPLQVLKACGAVDYFCQNGHGLISKKRVNFVISD --------10--------20--------30--------40--------50--------60--------70--