Solution structure of sf3636, a two-domain unknown function protein from Shigella flexneri 2a, determined by joint refinement of NMR, residual dipolar couplings and small-angle X-ray scatting, NESG target SfR339/OCSP target sf3636
MKEVEKNEIK RLSDRLDAIR HQQADLSLVE AADKYAELEK EKATLEAEIA RLREVHSQKL SKEAQKLMKM PFQRAITKKE QADMGKLKKS VRGLVVVHPM TALGREMGLE EMTGFSKTTF
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 96.2 % (1389 of 1444) | 96.7 % (740 of 765) | 95.5 % (529 of 554) | 96.0 % (120 of 125) |
Backbone | 96.8 % (693 of 716) | 97.1 % (236 of 243) | 96.9 % (344 of 355) | 95.8 % (113 of 118) |
Sidechain | 96.0 % (809 of 843) | 96.6 % (504 of 522) | 94.9 % (298 of 314) | 100.0 % (7 of 7) |
Aromatic | 76.0 % (38 of 50) | 92.0 % (23 of 25) | 60.0 % (15 of 25) | |
Methyl | 97.0 % (128 of 132) | 97.0 % (64 of 66) | 97.0 % (64 of 66) |
1. sf3636
MKEVEKNEIK RLSDRLDAIR HQQADLSLVE AADKYAELEK EKATLEAEIA RLREVHSQKL SKEAQKLMKM PFQRAITKKE QADMGKLKKS VRGLVVVHPM TALGREMGLE EMTGFSKTTFSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | sf3636 | [U-100% 13C; U-100% 15N] | 0.7 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | NaN3 | natural abundance | 0.01 % | |
7 | benzamidine | natural abundance | 10 mM | |
8 | inhibitor cocktail | natural abundance | 1 na | |
9 | H2O | natural abundance | 90 % | |
10 | D2O | natural abundance | 10 % |
Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
11 | sf3636 | [U-100% 13C; U-100% 15N] | 0.5 mM | |
12 | TRIS | [U-100% 2H] | 10 mM | |
13 | sodium chloride | natural abundance | 300 mM | |
14 | zinc sulphate | natural abundance | 10 uM | |
15 | DTT | [U-100% 2H] | 10 mM | |
16 | NaN3 | natural abundance | 0.01 % | |
17 | benzamidine | natural abundance | 10 mM | |
18 | inhibitor cocktail | natural abundance | 1 na | |
19 | D2O | natural abundance | 100 % |
Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
20 | sf3636 | [U-7% 13C; U-100% 15N] | 0.5 mM | |
21 | TRIS | [U-100% 2H] | 10 mM | |
22 | sodium chloride | natural abundance | 300 mM | |
23 | zinc sulphate | natural abundance | 10 uM | |
24 | DTT | [U-100% 2H] | 10 mM | |
25 | NaN3 | natural abundance | 0.01 % | |
26 | benzamidine | natural abundance | 10 mM | |
27 | inhibitor cocktail | natural abundance | 1 na | |
28 | H2O | natural abundance | 90 % | |
29 | 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 - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | sf3636 | [U-100% 13C; U-100% 15N] | 0.7 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | NaN3 | natural abundance | 0.01 % | |
7 | benzamidine | natural abundance | 10 mM | |
8 | inhibitor cocktail | natural abundance | 1 na | |
9 | H2O | natural abundance | 90 % | |
10 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | sf3636 | [U-100% 13C; U-100% 15N] | 0.7 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | NaN3 | natural abundance | 0.01 % | |
7 | benzamidine | natural abundance | 10 mM | |
8 | inhibitor cocktail | natural abundance | 1 na | |
9 | H2O | natural abundance | 90 % | |
10 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | sf3636 | [U-100% 13C; U-100% 15N] | 0.7 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | NaN3 | natural abundance | 0.01 % | |
7 | benzamidine | natural abundance | 10 mM | |
8 | inhibitor cocktail | natural abundance | 1 na | |
9 | H2O | natural abundance | 90 % | |
10 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | sf3636 | [U-100% 13C; U-100% 15N] | 0.7 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | NaN3 | natural abundance | 0.01 % | |
7 | benzamidine | natural abundance | 10 mM | |
8 | inhibitor cocktail | natural abundance | 1 na | |
9 | H2O | natural abundance | 90 % | |
10 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | sf3636 | [U-100% 13C; U-100% 15N] | 0.7 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | NaN3 | natural abundance | 0.01 % | |
7 | benzamidine | natural abundance | 10 mM | |
8 | inhibitor cocktail | natural abundance | 1 na | |
9 | H2O | natural abundance | 90 % | |
10 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | sf3636 | [U-100% 13C; U-100% 15N] | 0.7 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | NaN3 | natural abundance | 0.01 % | |
7 | benzamidine | natural abundance | 10 mM | |
8 | inhibitor cocktail | natural abundance | 1 na | |
9 | H2O | natural abundance | 90 % | |
10 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | sf3636 | [U-100% 13C; U-100% 15N] | 0.7 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | NaN3 | natural abundance | 0.01 % | |
7 | benzamidine | natural abundance | 10 mM | |
8 | inhibitor cocktail | natural abundance | 1 na | |
9 | H2O | natural abundance | 90 % | |
10 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | sf3636 | [U-100% 13C; U-100% 15N] | 0.7 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | NaN3 | natural abundance | 0.01 % | |
7 | benzamidine | natural abundance | 10 mM | |
8 | inhibitor cocktail | natural abundance | 1 na | |
9 | H2O | natural abundance | 90 % | |
10 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
11 | sf3636 | [U-100% 13C; U-100% 15N] | 0.5 mM | |
12 | TRIS | [U-100% 2H] | 10 mM | |
13 | sodium chloride | natural abundance | 300 mM | |
14 | zinc sulphate | natural abundance | 10 uM | |
15 | DTT | [U-100% 2H] | 10 mM | |
16 | NaN3 | natural abundance | 0.01 % | |
17 | benzamidine | natural abundance | 10 mM | |
18 | inhibitor cocktail | natural abundance | 1 na | |
19 | D2O | natural abundance | 100 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | sf3636 | [U-100% 13C; U-100% 15N] | 0.7 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | NaN3 | natural abundance | 0.01 % | |
7 | benzamidine | natural abundance | 10 mM | |
8 | inhibitor cocktail | natural abundance | 1 na | |
9 | H2O | natural abundance | 90 % | |
10 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
20 | sf3636 | [U-7% 13C; U-100% 15N] | 0.5 mM | |
21 | TRIS | [U-100% 2H] | 10 mM | |
22 | sodium chloride | natural abundance | 300 mM | |
23 | zinc sulphate | natural abundance | 10 uM | |
24 | DTT | [U-100% 2H] | 10 mM | |
25 | NaN3 | natural abundance | 0.01 % | |
26 | benzamidine | natural abundance | 10 mM | |
27 | inhibitor cocktail | natural abundance | 1 na | |
28 | H2O | natural abundance | 90 % | |
29 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | sf3636 | [U-100% 13C; U-100% 15N] | 0.7 mM | |
2 | TRIS | [U-100% 2H] | 10 mM | |
3 | sodium chloride | natural abundance | 300 mM | |
4 | zinc sulphate | natural abundance | 10 uM | |
5 | DTT | [U-100% 2H] | 10 mM | |
6 | NaN3 | natural abundance | 0.01 % | |
7 | benzamidine | natural abundance | 10 mM | |
8 | inhibitor cocktail | natural abundance | 1 na | |
9 | H2O | natural abundance | 90 % | |
10 | D2O | natural abundance | 10 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints | combined_17735_2lf0.nef |
Input source #2: Coordindates | 2lf0.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------- QGHMKEVEKNEIKRLSDRLDAIRHQQADLSLVEAADKYAELEKEKATLEAEIARLREVHSQKLSKEAQKLMKMPFQRAITKKEQADMGKLKKSVRGLVVV |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| QGHMKEVEKNEIKRLSDRLDAIRHQQADLSLVEAADKYAELEKEKATLEAEIARLREVHSQKLSKEAQKLMKMPFQRAITKKEQADMGKLKKSVRGLVVV --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 100-------110-------120 HPMTALGREMGLEEMTGFSKTTF ||||||||||||||||||||||| HPMTALGREMGLEEMTGFSKTTF -------110-------120---
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 123 | 0 | 0 | 100.0 |
Content subtype: combined_17735_2lf0.nef
Assigned chemical shifts
-----------10--------20--------30--------40--------50--------60--------70--------80--------90------- QGHMKEVEKNEIKRLSDRLDAIRHQQADLSLVEAADKYAELEKEKATLEAEIARLREVHSQKLSKEAQKLMKMPFQRAITKKEQADMGKLKKSVRGLVVV ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||| ....KEVEKNEIKRLSDRLDAIRHQQADLSLVEAADKYAELEKEKATLEAEIARLREVHSQKL.KEAQKLMKMPFQRAITKKEQADMGKLKKSVRGLVVV 100-------110-------120 HPMTALGREMGLEEMTGFSKTTF ||||||||||||||||||||||| HPMTALGREMGLEEMTGFSKTTF
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 782 | 739 | 94.5 |
13C chemical shifts | 565 | 528 | 93.5 |
15N chemical shifts | 137 | 120 | 87.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 250 | 235 | 94.0 |
13C chemical shifts | 246 | 230 | 93.5 |
15N chemical shifts | 121 | 112 | 92.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 532 | 504 | 94.7 |
13C chemical shifts | 319 | 298 | 93.4 |
15N chemical shifts | 16 | 8 | 50.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 73 | 70 | 95.9 |
13C chemical shifts | 73 | 70 | 95.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 27 | 23 | 85.2 |
13C chemical shifts | 27 | 15 | 55.6 |
Distance restraints
-----------10--------20--------30--------40--------50--------60--------70--------80--------90------- QGHMKEVEKNEIKRLSDRLDAIRHQQADLSLVEAADKYAELEKEKATLEAEIARLREVHSQKLSKEAQKLMKMPFQRAITKKEQADMGKLKKSVRGLVVV ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||| ....KEVEKNEIKRLSDRLDAIRHQQADLSLVEAADKYAELEKEKATLEAEIARLREVHSQKL.KEAQKLMKMPFQRAITKKEQADMGKLKKSVRGLVVV 100-------110-------120 HPMTALGREMGLEEMTGFSKTTF ||||||||||||||||||||||| HPMTALGREMGLEEMTGFSKTTF
-----------10--------20--------30--------40--------50--------60--------70--------80--------90------- QGHMKEVEKNEIKRLSDRLDAIRHQQADLSLVEAADKYAELEKEKATLEAEIARLREVHSQKLSKEAQKLMKMPFQRAITKKEQADMGKLKKSVRGLVVV |||||||||||||||||||| |||||||||||||||||||||||| ||||||||| | | ||| |||| || | | ........KNEIKRLSDRLDAIRHQQAD.......DKYAELEKEKATLEAEIARLREVH....SKEAQKLMK..F.R.ITK..QADM..LK......V.V -----------10--------20--------30--------40--------50--------60--------70--------80--------90------- 100-------110-------120 HPMTALGREMGLEEMTGFSKTTF || || ||||| ....AL..EM....MTGFS 100-------110------
Dihedral angle restraints
-----------10--------20--------30--------40--------50--------60--------70--------80--------90------- QGHMKEVEKNEIKRLSDRLDAIRHQQADLSLVEAADKYAELEKEKATLEAEIARLREVHSQKLSKEAQKLMKMPFQRAITKKEQADMGKLKKSVRGLVVV |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||| ||||| ......VEKNEIKRLSDRLDAIRHQQADLSLVEAADKYAELEKEKATLEAEIARLREVHSQKLSKEAQKLMK...QRAITKKEQADMGKLKKSV.GLVVV 100-------110-------120 HPMTALGREMGLEEMTGFSKTTF ||||||||||||||||||||||| HPMTALGREMGLEEMTGFSKTTF
RDC restraints
-----------10--------20--------30--------40--------50--------60--------70--------80--------90------- QGHMKEVEKNEIKRLSDRLDAIRHQQADLSLVEAADKYAELEKEKATLEAEIARLREVHSQKLSKEAQKLMKMPFQRAITKKEQADMGKLKKSVRGLVVV ||||| |||||||||||||||| |||||||||| |||||||||||||||||| |||||||| ||||||||| |||||||||||| |||| .......EKNEI..LSDRLDAIRHQQADLS.VEAADKYAEL.KEKATLEAEIARLREVHS....KEAQKLMK.PFQRAITKK.QADMGKLKKSVR.LVVV -----------10--------20--------30--------40--------50--------60--------70--------80--------90------- 100-------110-------120 HPMTALGREMGLEEMTGFSKTTF | |||||||||||||||||| H.MTALGREMGLEEMTGFSK 100-------110-------
-----------10--------20--------30--------40--------50--------60--------70--------80--------90------- QGHMKEVEKNEIKRLSDRLDAIRHQQADLSLVEAADKYAELEKEKATLEAEIARLREVHSQKLSKEAQKLMKMPFQRAITKKEQADMGKLKKSVRGLVVV |||||||||||||||||||||| ||||||||||||||||||||||||| |||||||| |||||||||||||||||||| |||| .......EKNEIKRLSDRLDAIRHQQADL.....ADKYAELEKEKATLEAEIARLREVH.....KEAQKLMK.PFQRAITKKEQADMGKLKKS...LVVV -----------10--------20--------30--------40--------50--------60--------70--------80--------90------- 100-------110-------120 HPMTALGREMGLEEMTGFSKTTF ||| ||||||| |||||| HPM.ALGREMG...MTGFSK 100-------110-------
-----------10--------20--------30--------40--------50--------60--------70--------80--------90------- QGHMKEVEKNEIKRLSDRLDAIRHQQADLSLVEAADKYAELEKEKATLEAEIARLREVHSQKLSKEAQKLMKMPFQRAITKKEQADMGKLKKSVRGLVVV | | | ||||||||| ||| |||| ||||||||||||||||| || | |||| ||||| | || ||||| |||| .......E..E..R.SDRLDAIRH.QAD......ADKY.ELEKEKATLEAEIARLR.VH......E..KLMK..FQRAI..K.QA..GKLKK....LVVV -----------10--------20--------30--------40--------50--------60--------70--------80--------90------- 100-------110-------120 HPMTALGREMGLEEMTGFSKTTF | ||||| |||| H....LGREM.....TGFS 100-------110------