Solution structure of the N-terminal domain of the effector NleG5-1 from Escherichia coli O157:H7 str. Sakai
MGSSHHHHHH SSGRENLYFQ GMPVDLTPYI LPGVSFLSDI PQETLSEIRN QTIRGEAQIR LGELMVSIRP MQVNGYFMGS LNQDGLSNDN IQIGLQYIEH IERTLNHGSL TSREVTVLRE IEMLENMDLL SNYQLEE
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 76.2 % (1218 of 1598) | 76.2 % (635 of 833) | 76.6 % (471 of 615) | 74.7 % (112 of 150) |
Backbone | 81.4 % (661 of 812) | 82.9 % (232 of 280) | 79.8 % (319 of 400) | 83.3 % (110 of 132) |
Sidechain | 72.3 % (659 of 912) | 72.9 % (403 of 553) | 74.5 % (254 of 341) | 11.1 % (2 of 18) |
Aromatic | 47.1 % (48 of 102) | 58.8 % (30 of 51) | 35.3 % (18 of 51) | |
Methyl | 93.3 % (140 of 150) | 94.7 % (71 of 75) | 92.0 % (69 of 75) |
1. entity 1
MGSSHHHHHH SSGRENLYFQ GMPVDLTPYI LPGVSFLSDI PQETLSEIRN QTIRGEAQIR LGELMVSIRP MQVNGYFMGS LNQDGLSNDN IQIGLQYIEH IERTLNHGSL TSREVTVLRE IEMLENMDLL SNYQLEESolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details 400 uM [U-100% 13C; U-100% 15N] NleG5-1, 15 mM HEPES, 250 mM sodium chloride, 5 mM L-arginine, 5 mM sodium citrate, 1 mM benzamidine, 10 uM DTT, 0.01 % w/v sodium azide, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DTT | natural abundance | 10 uM | |
2 | HEPES | natural abundance | 15 mM | |
3 | L-arginine | natural abundance | 5 mM | |
4 | NleG5-1 | [U-100% 13C; U-100% 15N] | 400 uM | |
5 | benzamidine | natural abundance | 1 mM | |
6 | sodium azide | natural abundance | 0.01 % w/v | |
7 | sodium chloride | natural abundance | 250 mM | |
8 | sodium citrate | natural abundance | 5 mM |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | external | indirect | 0.251 |
1H | DSS | methyl protons | 0.0 ppm | external | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | external | indirect | 0.101 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | external | indirect | 0.251 |
1H | DSS | methyl protons | 0.0 ppm | external | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | external | indirect | 0.101 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | external | indirect | 0.251 |
1H | DSS | methyl protons | 0.0 ppm | external | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | external | indirect | 0.101 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | external | indirect | 0.251 |
1H | DSS | methyl protons | 0.0 ppm | external | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | external | indirect | 0.101 |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details 400 uM [U-100% 13C; U-100% 15N] NleG5-1, 15 mM HEPES, 250 mM sodium chloride, 5 mM L-arginine, 5 mM sodium citrate, 1 mM benzamidine, 10 uM DTT, 0.01 % w/v sodium azide, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DTT | natural abundance | 10 uM | |
2 | HEPES | natural abundance | 15 mM | |
3 | L-arginine | natural abundance | 5 mM | |
4 | NleG5-1 | [U-100% 13C; U-100% 15N] | 400 uM | |
5 | benzamidine | natural abundance | 1 mM | |
6 | sodium azide | natural abundance | 0.01 % w/v | |
7 | sodium chloride | natural abundance | 250 mM | |
8 | sodium citrate | natural abundance | 5 mM |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details 400 uM [U-100% 13C; U-100% 15N] NleG5-1, 15 mM HEPES, 250 mM sodium chloride, 5 mM L-arginine, 5 mM sodium citrate, 1 mM benzamidine, 10 uM DTT, 0.01 % w/v sodium azide, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DTT | natural abundance | 10 uM | |
2 | HEPES | natural abundance | 15 mM | |
3 | L-arginine | natural abundance | 5 mM | |
4 | NleG5-1 | [U-100% 13C; U-100% 15N] | 400 uM | |
5 | benzamidine | natural abundance | 1 mM | |
6 | sodium azide | natural abundance | 0.01 % w/v | |
7 | sodium chloride | natural abundance | 250 mM | |
8 | sodium citrate | natural abundance | 5 mM |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details 400 uM [U-100% 13C; U-100% 15N] NleG5-1, 15 mM HEPES, 250 mM sodium chloride, 5 mM L-arginine, 5 mM sodium citrate, 1 mM benzamidine, 10 uM DTT, 0.01 % w/v sodium azide, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DTT | natural abundance | 10 uM | |
2 | HEPES | natural abundance | 15 mM | |
3 | L-arginine | natural abundance | 5 mM | |
4 | NleG5-1 | [U-100% 13C; U-100% 15N] | 400 uM | |
5 | benzamidine | natural abundance | 1 mM | |
6 | sodium azide | natural abundance | 0.01 % w/v | |
7 | sodium chloride | natural abundance | 250 mM | |
8 | sodium citrate | natural abundance | 5 mM |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details 400 uM [U-100% 13C; U-100% 15N] NleG5-1, 15 mM HEPES, 250 mM sodium chloride, 5 mM L-arginine, 5 mM sodium citrate, 1 mM benzamidine, 10 uM DTT, 0.01 % w/v sodium azide, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DTT | natural abundance | 10 uM | |
2 | HEPES | natural abundance | 15 mM | |
3 | L-arginine | natural abundance | 5 mM | |
4 | NleG5-1 | [U-100% 13C; U-100% 15N] | 400 uM | |
5 | benzamidine | natural abundance | 1 mM | |
6 | sodium azide | natural abundance | 0.01 % w/v | |
7 | sodium chloride | natural abundance | 250 mM | |
8 | sodium citrate | natural abundance | 5 mM |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details 400 uM [U-100% 13C; U-100% 15N] NleG5-1, 15 mM HEPES, 250 mM sodium chloride, 5 mM L-arginine, 5 mM sodium citrate, 1 mM benzamidine, 10 uM DTT, 0.01 % w/v sodium azide, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DTT | natural abundance | 10 uM | |
2 | HEPES | natural abundance | 15 mM | |
3 | L-arginine | natural abundance | 5 mM | |
4 | NleG5-1 | [U-100% 13C; U-100% 15N] | 400 uM | |
5 | benzamidine | natural abundance | 1 mM | |
6 | sodium azide | natural abundance | 0.01 % w/v | |
7 | sodium chloride | natural abundance | 250 mM | |
8 | sodium citrate | natural abundance | 5 mM |
Bruker AvanceII - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details 400 uM [U-100% 13C; U-100% 15N] NleG5-1, 15 mM HEPES, 250 mM sodium chloride, 5 mM L-arginine, 5 mM sodium citrate, 1 mM benzamidine, 10 uM DTT, 0.01 % w/v sodium azide, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DTT | natural abundance | 10 uM | |
2 | HEPES | natural abundance | 15 mM | |
3 | L-arginine | natural abundance | 5 mM | |
4 | NleG5-1 | [U-100% 13C; U-100% 15N] | 400 uM | |
5 | benzamidine | natural abundance | 1 mM | |
6 | sodium azide | natural abundance | 0.01 % w/v | |
7 | sodium chloride | natural abundance | 250 mM | |
8 | sodium citrate | natural abundance | 5 mM |
Bruker AvanceII - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details 400 uM [U-100% 13C; U-100% 15N] NleG5-1, 15 mM HEPES, 250 mM sodium chloride, 5 mM L-arginine, 5 mM sodium citrate, 1 mM benzamidine, 10 uM DTT, 0.01 % w/v sodium azide, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DTT | natural abundance | 10 uM | |
2 | HEPES | natural abundance | 15 mM | |
3 | L-arginine | natural abundance | 5 mM | |
4 | NleG5-1 | [U-100% 13C; U-100% 15N] | 400 uM | |
5 | benzamidine | natural abundance | 1 mM | |
6 | sodium azide | natural abundance | 0.01 % w/v | |
7 | sodium chloride | natural abundance | 250 mM | |
8 | sodium citrate | natural abundance | 5 mM |
Bruker AvanceII - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details 400 uM [U-100% 13C; U-100% 15N] NleG5-1, 15 mM HEPES, 250 mM sodium chloride, 5 mM L-arginine, 5 mM sodium citrate, 1 mM benzamidine, 10 uM DTT, 0.01 % w/v sodium azide, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DTT | natural abundance | 10 uM | |
2 | HEPES | natural abundance | 15 mM | |
3 | L-arginine | natural abundance | 5 mM | |
4 | NleG5-1 | [U-100% 13C; U-100% 15N] | 400 uM | |
5 | benzamidine | natural abundance | 1 mM | |
6 | sodium azide | natural abundance | 0.01 % w/v | |
7 | sodium chloride | natural abundance | 250 mM | |
8 | sodium citrate | natural abundance | 5 mM |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details 400 uM [U-100% 13C; U-100% 15N] NleG5-1, 15 mM HEPES, 250 mM sodium chloride, 5 mM L-arginine, 5 mM sodium citrate, 1 mM benzamidine, 10 uM DTT, 0.01 % w/v sodium azide, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DTT | natural abundance | 10 uM | |
2 | HEPES | natural abundance | 15 mM | |
3 | L-arginine | natural abundance | 5 mM | |
4 | NleG5-1 | [U-100% 13C; U-100% 15N] | 400 uM | |
5 | benzamidine | natural abundance | 1 mM | |
6 | sodium azide | natural abundance | 0.01 % w/v | |
7 | sodium chloride | natural abundance | 250 mM | |
8 | sodium citrate | natural abundance | 5 mM |
Bruker AvanceII - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details 400 uM [U-100% 13C; U-100% 15N] NleG5-1, 15 mM HEPES, 250 mM sodium chloride, 5 mM L-arginine, 5 mM sodium citrate, 1 mM benzamidine, 10 uM DTT, 0.01 % w/v sodium azide, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DTT | natural abundance | 10 uM | |
2 | HEPES | natural abundance | 15 mM | |
3 | L-arginine | natural abundance | 5 mM | |
4 | NleG5-1 | [U-100% 13C; U-100% 15N] | 400 uM | |
5 | benzamidine | natural abundance | 1 mM | |
6 | sodium azide | natural abundance | 0.01 % w/v | |
7 | sodium chloride | natural abundance | 250 mM | |
8 | sodium citrate | natural abundance | 5 mM |
Bruker AvanceII - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details 400 uM [U-100% 13C; U-100% 15N] NleG5-1, 15 mM HEPES, 250 mM sodium chloride, 5 mM L-arginine, 5 mM sodium citrate, 1 mM benzamidine, 10 uM DTT, 0.01 % w/v sodium azide, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DTT | natural abundance | 10 uM | |
2 | HEPES | natural abundance | 15 mM | |
3 | L-arginine | natural abundance | 5 mM | |
4 | NleG5-1 | [U-100% 13C; U-100% 15N] | 400 uM | |
5 | benzamidine | natural abundance | 1 mM | |
6 | sodium azide | natural abundance | 0.01 % w/v | |
7 | sodium chloride | natural abundance | 250 mM | |
8 | sodium citrate | natural abundance | 5 mM |
Bruker AvanceII - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details 400 uM [U-100% 13C; U-100% 15N] NleG5-1, 15 mM HEPES, 250 mM sodium chloride, 5 mM L-arginine, 5 mM sodium citrate, 1 mM benzamidine, 10 uM DTT, 0.01 % w/v sodium azide, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DTT | natural abundance | 10 uM | |
2 | HEPES | natural abundance | 15 mM | |
3 | L-arginine | natural abundance | 5 mM | |
4 | NleG5-1 | [U-100% 13C; U-100% 15N] | 400 uM | |
5 | benzamidine | natural abundance | 1 mM | |
6 | sodium azide | natural abundance | 0.01 % w/v | |
7 | sodium chloride | natural abundance | 250 mM | |
8 | sodium citrate | natural abundance | 5 mM |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints | combined_30348_6b3n.nef |
Input source #2: Coordindates | 6b3n.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--------8 MGSSHHHHHHSSGRENLYFQGMPVDLTPYILPGVSFLSDIPQETLSEIRNQTIRGEAQIRLGELMVSIRPMQVNGYFMGSLNQDGLSNDNIQIGLQYIEH |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MGSSHHHHHHSSGRENLYFQGMPVDLTPYILPGVSFLSDIPQETLSEIRNQTIRGEAQIRLGELMVSIRPMQVNGYFMGSLNQDGLSNDNIQIGLQYIEH --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 0--------90-------100-------110------ IERTLNHGSLTSREVTVLREIEMLENMDLLSNYQLEE ||||||||||||||||||||||||||||||||||||| IERTLNHGSLTSREVTVLREIEMLENMDLLSNYQLEE -------110-------120-------130-------
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 137 | 0 | 0 | 100.0 |
Content subtype: combined_30348_6b3n.nef
Assigned chemical shifts
-----------------------------10--------20--------30--------40--------50--------60--------70--------8 MGSSHHHHHHSSGRENLYFQGMPVDLTPYILPGVSFLSDIPQETLSEIRNQTIRGEAQIRLGELMVSIRPMQVNGYFMGSLNQDGLSNDNIQIGLQYIEH ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| .....................MPVDLTPYILPGVSFLSDIPQETLSEIRNQTIRGEAQIRLGELMVSIRPMQVNGYFMGSLNQDGLSNDNIQIGLQYIEH 0--------90-------100-------110------ IERTLNHGSLTSREVTVLREIEMLENMDLLSNYQLEE |||||||||||||||||| |||||||||||| ||||| IERTLNHGSLTSREVTVL.EIEMLENMDLLS.YQLEE
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 833 | 581 | 69.7 |
15N chemical shifts | 158 | 97 | 61.4 |
13C chemical shifts | 615 | 438 | 71.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 280 | 214 | 76.4 |
15N chemical shifts | 132 | 97 | 73.5 |
13C chemical shifts | 274 | 204 | 74.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 553 | 367 | 66.4 |
15N chemical shifts | 26 | 0 | 0.0 |
13C chemical shifts | 341 | 234 | 68.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 82 | 68 | 82.9 |
13C chemical shifts | 82 | 68 | 82.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 51 | 16 | 31.4 |
13C chemical shifts | 51 | 8 | 15.7 |
Distance restraints
-----------------------------10--------20--------30--------40--------50--------60--------70--------8 MGSSHHHHHHSSGRENLYFQGMPVDLTPYILPGVSFLSDIPQETLSEIRNQTIRGEAQIRLGELMVSIRPMQVNGYFMGSLNQDGLSNDNIQIGLQYIEH ||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||| ......................PVDLTPYILPGVSFLSDIP.ETLSEIRNQTIRGEAQIRLGELMVSIRPM..NGYFMGSLNQDGLSNDNIQIGLQYIEH -----------------------------10--------20--------30--------40--------50--------60--------70--------8 0--------90-------100-------110------ IERTLNHGSLTSREVTVLREIEMLENMDLLSNYQLEE |||||| ||||||||||| || IERTLN.GSLTSREVTVL.EI 0--------90-------100