Solution NMR Structure of NifU-like protein from Saccharomyces cerevisiae, Northeast Structural Genomics Consortium (NESG) Target YR313A
MGHHHHHHSH MNSQRLIHIK TLTTPNENAL KFLSTDGEML QTRGSKSIVI KNTDENLINH SKLAQQIFLQ CPGVESLMIG DDFLTINKDR MVHWNSIKPE IIDLLTKQLA YGEDVISKE
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 84.1 % (1191 of 1417) | 90.4 % (667 of 738) | 73.9 % (405 of 548) | 90.8 % (119 of 131) |
Backbone | 78.2 % (554 of 708) | 90.5 % (218 of 241) | 66.1 % (232 of 351) | 89.7 % (104 of 116) |
Sidechain | 90.1 % (741 of 822) | 90.3 % (449 of 497) | 89.4 % (277 of 310) | 100.0 % (15 of 15) |
Aromatic | 58.9 % (53 of 90) | 60.0 % (27 of 45) | 56.8 % (25 of 44) | 100.0 % (1 of 1) |
Methyl | 100.0 % (138 of 138) | 100.0 % (69 of 69) | 100.0 % (69 of 69) |
1. YR313A
MGHHHHHHSH MNSQRLIHIK TLTTPNENAL KFLSTDGEML QTRGSKSIVI KNTDENLINH SKLAQQIFLQ CPGVESLMIG DDFLTINKDR MVHWNSIKPE IIDLLTKQLA YGEDVISKESolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.027 mM YR313A.037, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | YR313A.037 | [U-100% 13C; U-100% 15N] | 1.027 mM | |
2 | NaCl | natural abundance | 450 mM | |
3 | Na2PO4 | natural abundance | 25 mM | |
4 | DTT | natural abundance | 10 mM | |
5 | ZnSO4 | natural abundance | 20 uM | |
6 | Proteinase inhibitors | natural abundance | 1 na | |
7 | NaN3 | natural abundance | 0.02 % | |
8 | D2O | natural abundance | 10 % | |
9 | H2O | natural abundance | 90 % |
Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.52 mM YR313A.037, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
10 | YR313A.040 | [U-10% 13C; U-100% 15N] | 0.52 mM | |
11 | NaCl | natural abundance | 450 mM | |
12 | Na2PO4 | natural abundance | 25 mM | |
13 | DTT | natural abundance | 10 mM | |
14 | ZnSO4 | natural abundance | 20 uM | |
15 | Proteinase inhibitors | natural abundance | 1 na | |
16 | NaN3 | natural abundance | 0.02 % | |
17 | D2O | natural abundance | 10 % | |
18 | H2O | natural abundance | 90 % |
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 |
Pressure 1 atm, Temperature 298 K, pH 6.5
Experiment name 2D 1H-15N HSQC
List #1 RDC_list_1, RDC code DHN, Field strength (1H) 599.520 MHz, Details two alignment media: peg (ori 1) and phage (ori 2)
List #2 RDC_list_12, RDC code DHN, Field strength (1H) 599.520 MHz, Details two alignment media: peg (ori 1) and phage (ori 2)
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.027 mM YR313A.037, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | YR313A.037 | [U-100% 13C; U-100% 15N] | 1.027 mM | |
2 | NaCl | natural abundance | 450 mM | |
3 | Na2PO4 | natural abundance | 25 mM | |
4 | DTT | natural abundance | 10 mM | |
5 | ZnSO4 | natural abundance | 20 uM | |
6 | Proteinase inhibitors | natural abundance | 1 na | |
7 | NaN3 | natural abundance | 0.02 % | |
8 | D2O | natural abundance | 10 % | |
9 | H2O | natural abundance | 90 % |
Varian INOVA - 600 MHz at Rutgers
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.52 mM YR313A.037, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
10 | YR313A.040 | [U-10% 13C; U-100% 15N] | 0.52 mM | |
11 | NaCl | natural abundance | 450 mM | |
12 | Na2PO4 | natural abundance | 25 mM | |
13 | DTT | natural abundance | 10 mM | |
14 | ZnSO4 | natural abundance | 20 uM | |
15 | Proteinase inhibitors | natural abundance | 1 na | |
16 | NaN3 | natural abundance | 0.02 % | |
17 | D2O | natural abundance | 10 % | |
18 | H2O | natural abundance | 90 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.027 mM YR313A.037, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | YR313A.037 | [U-100% 13C; U-100% 15N] | 1.027 mM | |
2 | NaCl | natural abundance | 450 mM | |
3 | Na2PO4 | natural abundance | 25 mM | |
4 | DTT | natural abundance | 10 mM | |
5 | ZnSO4 | natural abundance | 20 uM | |
6 | Proteinase inhibitors | natural abundance | 1 na | |
7 | NaN3 | natural abundance | 0.02 % | |
8 | D2O | natural abundance | 10 % | |
9 | H2O | natural abundance | 90 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.027 mM YR313A.037, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | YR313A.037 | [U-100% 13C; U-100% 15N] | 1.027 mM | |
2 | NaCl | natural abundance | 450 mM | |
3 | Na2PO4 | natural abundance | 25 mM | |
4 | DTT | natural abundance | 10 mM | |
5 | ZnSO4 | natural abundance | 20 uM | |
6 | Proteinase inhibitors | natural abundance | 1 na | |
7 | NaN3 | natural abundance | 0.02 % | |
8 | D2O | natural abundance | 10 % | |
9 | H2O | natural abundance | 90 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.027 mM YR313A.037, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | YR313A.037 | [U-100% 13C; U-100% 15N] | 1.027 mM | |
2 | NaCl | natural abundance | 450 mM | |
3 | Na2PO4 | natural abundance | 25 mM | |
4 | DTT | natural abundance | 10 mM | |
5 | ZnSO4 | natural abundance | 20 uM | |
6 | Proteinase inhibitors | natural abundance | 1 na | |
7 | NaN3 | natural abundance | 0.02 % | |
8 | D2O | natural abundance | 10 % | |
9 | H2O | natural abundance | 90 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.027 mM YR313A.037, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | YR313A.037 | [U-100% 13C; U-100% 15N] | 1.027 mM | |
2 | NaCl | natural abundance | 450 mM | |
3 | Na2PO4 | natural abundance | 25 mM | |
4 | DTT | natural abundance | 10 mM | |
5 | ZnSO4 | natural abundance | 20 uM | |
6 | Proteinase inhibitors | natural abundance | 1 na | |
7 | NaN3 | natural abundance | 0.02 % | |
8 | D2O | natural abundance | 10 % | |
9 | H2O | natural abundance | 90 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.027 mM YR313A.037, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | YR313A.037 | [U-100% 13C; U-100% 15N] | 1.027 mM | |
2 | NaCl | natural abundance | 450 mM | |
3 | Na2PO4 | natural abundance | 25 mM | |
4 | DTT | natural abundance | 10 mM | |
5 | ZnSO4 | natural abundance | 20 uM | |
6 | Proteinase inhibitors | natural abundance | 1 na | |
7 | NaN3 | natural abundance | 0.02 % | |
8 | D2O | natural abundance | 10 % | |
9 | H2O | natural abundance | 90 % |
Varian INOVA - 600 MHz at UGA
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.52 mM YR313A.037, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
10 | YR313A.040 | [U-10% 13C; U-100% 15N] | 0.52 mM | |
11 | NaCl | natural abundance | 450 mM | |
12 | Na2PO4 | natural abundance | 25 mM | |
13 | DTT | natural abundance | 10 mM | |
14 | ZnSO4 | natural abundance | 20 uM | |
15 | Proteinase inhibitors | natural abundance | 1 na | |
16 | NaN3 | natural abundance | 0.02 % | |
17 | D2O | natural abundance | 10 % | |
18 | H2O | natural abundance | 90 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.027 mM YR313A.037, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | YR313A.037 | [U-100% 13C; U-100% 15N] | 1.027 mM | |
2 | NaCl | natural abundance | 450 mM | |
3 | Na2PO4 | natural abundance | 25 mM | |
4 | DTT | natural abundance | 10 mM | |
5 | ZnSO4 | natural abundance | 20 uM | |
6 | Proteinase inhibitors | natural abundance | 1 na | |
7 | NaN3 | natural abundance | 0.02 % | |
8 | D2O | natural abundance | 10 % | |
9 | H2O | natural abundance | 90 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_18487_2ltl.nef |
Input source #2: Coordindates | 2ltl.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 MGHHHHHHSHMNSQRLIHIKTLTTPNENALKFLSTDGEMLQTRGSKSIVIKNTDENLINHSKLAQQIFLQCPGVESLMIGDDFLTINKDRMVHWNSIKPE |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MGHHHHHHSHMNSQRLIHIKTLTTPNENALKFLSTDGEMLQTRGSKSIVIKNTDENLINHSKLAQQIFLQCPGVESLMIGDDFLTINKDRMVHWNSIKPE -------110--------- IIDLLTKQLAYGEDVISKE ||||||||||||||||||| IIDLLTKQLAYGEDVISKE
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 119 | 0 | 0 | 100.0 |
Content subtype: combined_18487_2ltl.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MGHHHHHHSHMNSQRLIHIKTLTTPNENALKFLSTDGEMLQTRGSKSIVIKNTDENLINHSKLAQQIFLQCPGVESLMIGDDFLTINKDRMVHWNSIKPE ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| .........HMNSQRLIHIKTLTTPNENALKFLSTDGEMLQTRGSKSIVIKNTDENLINHSKLAQQIFLQCPGVESLMIGDDFLTINKDRMVHWNSIKPE -------110--------- IIDLLTKQLAYGEDVISKE ||||||||||||||||||| IIDLLTKQLAYGEDVISKE
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 738 | 668 | 90.5 |
13C chemical shifts | 548 | 386 | 70.4 |
15N chemical shifts | 134 | 119 | 88.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 241 | 219 | 90.9 |
13C chemical shifts | 238 | 109 | 45.8 |
15N chemical shifts | 116 | 104 | 89.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 497 | 449 | 90.3 |
13C chemical shifts | 310 | 277 | 89.4 |
15N chemical shifts | 18 | 15 | 83.3 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 74 | 72 | 97.3 |
13C chemical shifts | 74 | 72 | 97.3 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 45 | 27 | 60.0 |
13C chemical shifts | 44 | 25 | 56.8 |
15N chemical shifts | 1 | 1 | 100.0 |
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MGHHHHHHSHMNSQRLIHIKTLTTPNENALKFLSTDGEMLQTRGSKSIVIKNTDENLINHSKLAQQIFLQCPGVESLMIGDDFLTINKDRMVHWNSIKPE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ..........M..QRLIHIKTLTTPNENALKFLSTDGEMLQTRGSKSIVIKNTDENLINHSKLAQQIFLQCPGVESLMIGDDFLTINKDRMVHWNSIKPE -------110--------- IIDLLTKQLAYGEDVISKE ||||||||||||||||||| IIDLLTKQLAYGEDVISKE
Dihedral angle restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MGHHHHHHSHMNSQRLIHIKTLTTPNENALKFLSTDGEMLQTRGSKSIVIKNTDENLINHSKLAQQIFLQCPGVESLMIGDDFLTINKDRMVHWNSIKPE ||||||||| |||||||| |||||| |||||||||||||||||| ||||||| ||||||||| |||||||| ...............LIHIKTLTT...NALKFLST...........SIVIKN.DENLINHSKLAQQIFLQC..VESLMIG.DFLTINKDR..HWNSIKPE --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -------110--------- IIDLLTKQLAYGEDVISKE |||||||||||| IIDLLTKQLAYG -------110--