Solution structure of the E. coli outer membrane protein RcsF (periplasmatic domain)
MAPQPKAEPA KPKAPRATPV RIYTNAEELV GKPFRDLGEV SGDSCQASNQ DSPPSIPTAR KRMQINASKM KANAVLLHSC EVTSGTPGCY RQAVCIGSAL NITAK
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | disulfide | sing | 1:CYS45:SG | 1:CYS89:SG |
2 | disulfide | sing | 1:CYS80:SG | 1:CYS95:SG |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 86.0 % (999 of 1161) | 83.0 % (507 of 611) | 91.0 % (406 of 446) | 82.7 % (86 of 104) |
Backbone | 90.0 % (547 of 608) | 87.8 % (180 of 205) | 91.9 % (284 of 309) | 88.3 % (83 of 94) |
Sidechain | 82.1 % (535 of 652) | 79.1 % (321 of 406) | 89.4 % (211 of 236) | 30.0 % (3 of 10) |
Aromatic | 100.0 % (30 of 30) | 100.0 % (15 of 15) | 100.0 % (15 of 15) | |
Methyl | 92.3 % (96 of 104) | 88.5 % (46 of 52) | 96.2 % (50 of 52) |
1. RcsF
MAPQPKAEPA KPKAPRATPV RIYTNAEELV GKPFRDLGEV SGDSCQASNQ DSPPSIPTAR KRMQINASKM KANAVLLHSC EVTSGTPGCY RQAVCIGSAL NITAKSolvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | RcsF(31-134) | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | protease inhibitors cocktail | natural abundance | 4.6 mM | |
5 | DSS | natural abundance | 0.3 mM |
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 |
Bruker Avance - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | RcsF(31-134) | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | protease inhibitors cocktail | natural abundance | 4.6 mM | |
5 | DSS | natural abundance | 0.3 mM |
Bruker Avance - 900 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | RcsF(31-134) | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | protease inhibitors cocktail | natural abundance | 4.6 mM | |
5 | DSS | natural abundance | 0.3 mM |
Bruker Avance - 900 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | RcsF(31-134) | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | protease inhibitors cocktail | natural abundance | 4.6 mM | |
5 | DSS | natural abundance | 0.3 mM |
Bruker Avance - 700 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | RcsF(31-134) | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | protease inhibitors cocktail | natural abundance | 4.6 mM | |
5 | DSS | natural abundance | 0.3 mM |
Bruker Avance - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | RcsF(31-134) | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | protease inhibitors cocktail | natural abundance | 4.6 mM | |
5 | DSS | natural abundance | 0.3 mM |
Bruker Avance - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | RcsF(31-134) | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | protease inhibitors cocktail | natural abundance | 4.6 mM | |
5 | DSS | natural abundance | 0.3 mM |
Bruker Avance - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | RcsF(31-134) | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | protease inhibitors cocktail | natural abundance | 4.6 mM | |
5 | DSS | natural abundance | 0.3 mM |
Bruker Avance - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | RcsF(31-134) | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | protease inhibitors cocktail | natural abundance | 4.6 mM | |
5 | DSS | natural abundance | 0.3 mM |
Bruker Avance - 900 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | RcsF(31-134) | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | protease inhibitors cocktail | natural abundance | 4.6 mM | |
5 | DSS | natural abundance | 0.3 mM |
Bruker Avance - 900 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | RcsF(31-134) | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | protease inhibitors cocktail | natural abundance | 4.6 mM | |
5 | DSS | natural abundance | 0.3 mM |
Bruker Avance - 800 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | RcsF(31-134) | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | protease inhibitors cocktail | natural abundance | 4.6 mM | |
5 | DSS | natural abundance | 0.3 mM |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_17431_2l8y.nef |
Input source #2: Coordindates | 2l8y.cif |
Diamagnetism of the molecular assembly | True (excluding Oxygen atoms) |
Whether the assembly has a disulfide bond | True (see coordinates for details) |
Whether the assembly has a other bond | None |
Whether the assembly contains a cyclic polymer | None |
Overall data processing status | Warning |
Disulfide bonds
Ptnr_site_1 | Ptnr_site_2 | Redox_state_prediction_1 | Redox_state_prediction_2 | Distance (Å) |
---|---|---|---|---|
A:74:CYS:SG | A:118:CYS:SG | oxidized, CA 55.3, CB 45.1 ppm | oxidized, CA 54.8, CB 44.3 ppm | 2.032 |
A:109:CYS:SG | A:124:CYS:SG | oxidized, CA 56.5, CB 48.8 ppm | oxidized, CA 55.3, CB 46.2 ppm | 2.033 |
Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
NoneSequence alignments
30-------40--------50--------60--------70--------80--------90-------100-------110-------120-------13 MAPQPKAEPAKPKAPRATPVRIYTNAEELVGKPFRDLGEVSGDSCQASNQDSPPSIPTARKRMQINASKMKANAVLLHSCEVTSGTPGCYRQAVCIGSAL |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MAPQPKAEPAKPKAPRATPVRIYTNAEELVGKPFRDLGEVSGDSCQASNQDSPPSIPTARKRMQINASKMKANAVLLHSCEVTSGTPGCYRQAVCIGSAL --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 0---- NITAK ||||| NITAK -----
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 105 | 0 | 0 | 100.0 |
Content subtype: combined_17431_2l8y.nef
Assigned chemical shifts
30-------40--------50--------60--------70--------80--------90-------100-------110-------120-------13 MAPQPKAEPAKPKAPRATPVRIYTNAEELVGKPFRDLGEVSGDSCQASNQDSPPSIPTARKRMQINASKMKANAVLLHSCEVTSGTPGCYRQAVCIGSAL ||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MAPQPKAEPAK.KA...TPVRIYTNAEELVGKPFRDLGEVSGDSCQASNQDSPPSIPTARKRMQINASKMKANAVLLHSCEVTSGTPGCYRQAVCIGSAL 0---- NITAK ||||| NITAK
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 611 | 507 | 83.0 |
13C chemical shifts | 446 | 403 | 90.4 |
15N chemical shifts | 110 | 86 | 78.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 205 | 185 | 90.2 |
13C chemical shifts | 210 | 194 | 92.4 |
15N chemical shifts | 94 | 83 | 88.3 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 406 | 322 | 79.3 |
13C chemical shifts | 236 | 209 | 88.6 |
15N chemical shifts | 16 | 3 | 18.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 55 | 52 | 94.5 |
13C chemical shifts | 55 | 53 | 96.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 15 | 15 | 100.0 |
13C chemical shifts | 15 | 15 | 100.0 |
Covalent bonds
Distance restraints
30-------40--------50--------60--------70--------80--------90-------100-------110-------120-------13 MAPQPKAEPAKPKAPRATPVRIYTNAEELVGKPFRDLGEVSGDSCQASNQDSPPSIPTARKRMQINASKMKANAVLLHSCEVTSGTPGCYRQAVCIGSAL ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| .................TPVRIYTNAEELVGKPFRDLGEVSGDSCQASNQDSPPSIPTARKRMQINASKMKANAVLLHSCEVTSGTPGCYRQAVCIGSAL 0---- NITAK ||||| NITAK
30-------40--------50--------60--------70--------80--------90-------100-------110-------120-------13 MAPQPKAEPAKPKAPRATPVRIYTNAEELVGKPFRDLGEVSGDSCQASNQDSPPSIPTARKRMQINASKMKANAVLLHSCEVTSGTPGCYRQAVCIGSAL | | || |||||| | | | | | | ||||||||||||||| ||||||| | | | ||||||||||| ....................R.Y.NA.ELVGKP.R..G.V.G.S.Q........SIPTARKRMQINASK...NAVLLHS.E.T.G....YRQAVCIGSAL 30-------40--------50--------60--------70--------80--------90-------100-------110-------120-------13 0---- NITAK | | N.T 0--
Dihedral angle restraints
30-------40--------50--------60--------70--------80--------90-------100-------110-------120-------13 MAPQPKAEPAKPKAPRATPVRIYTNAEELVGKPFRDLGEVSGDSCQASNQDSPPSIPTARKRMQINASKMKANAVLLHSCEVTSGTPGCYRQAVCIGSAL ||||||||||||| ||||||||||||||||||||| |||||||||||||||| ||||||||||||| ||||||||||| ..................PVRIYTNAEELVG.PFRDLGEVSGDSCQASNQDSP.SIPTARKRMQINASKM..NAVLLHSCEVTSG....YRQAVCIGSAL 0---- NITAK ||||| NITAK