NMR structure of the Paracoccus denitrificans Z-subunit determined in the presence of ADP
MTTFDDRERA HEAKFAHDAE LNFKAEARRN RLLGEWAAGL LGKTGDDARA YALTVVTSDF DEPGDEDVFR KLAADLEGKA DEETIRAKMV ELRATAREQI ISEI
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 84.6 % (987 of 1167) | 83.3 % (503 of 604) | 84.4 % (385 of 456) | 92.5 % (99 of 107) |
Backbone | 87.0 % (541 of 622) | 89.7 % (191 of 213) | 83.3 % (255 of 306) | 92.2 % (95 of 103) |
Sidechain | 82.3 % (529 of 643) | 79.0 % (309 of 391) | 87.1 % (216 of 248) | 100.0 % (4 of 4) |
Aromatic | 67.9 % (53 of 78) | 66.7 % (26 of 39) | 68.4 % (26 of 38) | 100.0 % (1 of 1) |
Methyl | 94.8 % (110 of 116) | 94.8 % (55 of 58) | 94.8 % (55 of 58) |
1. Z-subunit
MTTFDDRERA HEAKFAHDAE LNFKAEARRN RLLGEWAAGL LGKTGDDARA YALTVVTSDF DEPGDEDVFR KLAADLEGKA DEETIRAKMV ELRATAREQI ISEISolvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Z-subunit | [U-98% 13C; U-98% 15N] | 1.5 mM | |
2 | sodium chloride | natural abundance | 50 mM | |
3 | sodium phosphate | natural abundance | 25 mM | |
4 | sodium azide | natural abundance | 5 mM | |
5 | ADP | natural abundance | 10 mM | |
6 | H2O | natural abundance | 95 % | |
7 | D2O | natural abundance | 5 % |
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
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Z-subunit | [U-98% 13C; U-98% 15N] | 1.5 mM | |
2 | sodium chloride | natural abundance | 50 mM | |
3 | sodium phosphate | natural abundance | 25 mM | |
4 | sodium azide | natural abundance | 5 mM | |
5 | ADP | natural abundance | 10 mM | |
6 | H2O | natural abundance | 95 % | |
7 | D2O | natural abundance | 5 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Z-subunit | [U-98% 13C; U-98% 15N] | 1.5 mM | |
2 | sodium chloride | natural abundance | 50 mM | |
3 | sodium phosphate | natural abundance | 25 mM | |
4 | sodium azide | natural abundance | 5 mM | |
5 | ADP | natural abundance | 10 mM | |
6 | H2O | natural abundance | 95 % | |
7 | D2O | natural abundance | 5 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Z-subunit | [U-98% 13C; U-98% 15N] | 1.5 mM | |
2 | sodium chloride | natural abundance | 50 mM | |
3 | sodium phosphate | natural abundance | 25 mM | |
4 | sodium azide | natural abundance | 5 mM | |
5 | ADP | natural abundance | 10 mM | |
6 | H2O | natural abundance | 95 % | |
7 | D2O | natural abundance | 5 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Z-subunit | [U-98% 13C; U-98% 15N] | 1.5 mM | |
2 | sodium chloride | natural abundance | 50 mM | |
3 | sodium phosphate | natural abundance | 25 mM | |
4 | sodium azide | natural abundance | 5 mM | |
5 | ADP | natural abundance | 10 mM | |
6 | H2O | natural abundance | 95 % | |
7 | D2O | natural abundance | 5 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Z-subunit | [U-98% 13C; U-98% 15N] | 1.5 mM | |
2 | sodium chloride | natural abundance | 50 mM | |
3 | sodium phosphate | natural abundance | 25 mM | |
4 | sodium azide | natural abundance | 5 mM | |
5 | ADP | natural abundance | 10 mM | |
6 | H2O | natural abundance | 95 % | |
7 | D2O | natural abundance | 5 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Z-subunit | [U-98% 13C; U-98% 15N] | 1.5 mM | |
2 | sodium chloride | natural abundance | 50 mM | |
3 | sodium phosphate | natural abundance | 25 mM | |
4 | sodium azide | natural abundance | 5 mM | |
5 | ADP | natural abundance | 10 mM | |
6 | H2O | natural abundance | 95 % | |
7 | D2O | natural abundance | 5 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Z-subunit | [U-98% 13C; U-98% 15N] | 1.5 mM | |
2 | sodium chloride | natural abundance | 50 mM | |
3 | sodium phosphate | natural abundance | 25 mM | |
4 | sodium azide | natural abundance | 5 mM | |
5 | ADP | natural abundance | 10 mM | |
6 | H2O | natural abundance | 95 % | |
7 | D2O | natural abundance | 5 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints | combined_19510_2mdz.nef |
Input source #2: Coordindates | 2mdz.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 MTTFDDRERAHEAKFAHDAELNFKAEARRNRLLGEWAAGLLGKTGDDARAYALTVVTSDFDEPGDEDVFRKLAADLEGKADEETIRAKMVELRATAREQI |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MTTFDDRERAHEAKFAHDAELNFKAEARRNRLLGEWAAGLLGKTGDDARAYALTVVTSDFDEPGDEDVFRKLAADLEGKADEETIRAKMVELRATAREQI ---- ISEI |||| ISEI
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 104 | 0 | 0 | 100.0 |
Content subtype: combined_19510_2mdz.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MTTFDDRERAHEAKFAHDAELNFKAEARRNRLLGEWAAGLLGKTGDDARAYALTVVTSDFDEPGDEDVFRKLAADLEGKADEETIRAKMVELRATAREQI | |||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| ...F..RERAHEAKFAHDAELNFKAEARRNRLLGEWAAGLLGKTGDDARAYALTVVTSDF..PGDEDVFRKLAADLEGKADEETIRAKMVELRATAREQI ---- ISEI |||| ISEI
Comp_index_ID | Comp_ID | Atom_ID | CS value (ppm) |
---|---|---|---|
9 | ARG | NH2 | 115.742 |
28 | ARG | NH2 | 114.96 |
29 | ARG | NH2 | 110.625 |
31 | ARG | NH2 | 114.684 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 604 | 510 | 84.4 |
13C chemical shifts | 456 | 381 | 83.6 |
15N chemical shifts | 117 | 99 | 84.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 213 | 198 | 93.0 |
13C chemical shifts | 208 | 162 | 77.9 |
15N chemical shifts | 103 | 95 | 92.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 391 | 312 | 79.8 |
13C chemical shifts | 248 | 219 | 88.3 |
15N chemical shifts | 14 | 4 | 28.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 60 | 57 | 95.0 |
13C chemical shifts | 60 | 57 | 95.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 39 | 26 | 66.7 |
13C chemical shifts | 38 | 26 | 68.4 |
15N chemical shifts | 1 | 1 | 100.0 |
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MTTFDDRERAHEAKFAHDAELNFKAEARRNRLLGEWAAGLLGKTGDDARAYALTVVTSDFDEPGDEDVFRKLAADLEGKADEETIRAKMVELRATAREQI | |||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||| ...F..RERAHEAKFAHDAELNFKAEARRNRLLGEWAAGLLGKTGDDARAYALTVVTSDF...GDEDVFRKLAADLEGKADEETIRAKMVELRATAREQI ---- ISEI |||| ISEI