Solution structure of the MRH domain of Yos9 complexed with alpha3,alpha6-Man5
GASNSEKTAL LTKTLNQGVK TIFDKLNERC IFYQAGFWIY EYCPGIEFVQ FHGRVNTKTG EIVNRDESLV YRLGKPKANV EEREFELLYD DVGYYISEII GSGDICDVTG AERMVEIQYV CGGSNSGPST IQWVRETKIC VYEAQVTIPE LCNLELLAKN ED
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | disulfide | sing | 1:CYS30:SG | 1:CYS43:SG |
2 | disulfide | sing | 1:CYS106:SG | 1:CYS140:SG |
3 | disulfide | sing | 1:CYS121:SG | 1:CYS152:SG |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 90.0 % (1700 of 1888) | 89.5 % (874 of 977) | 91.8 % (676 of 736) | 85.7 % (150 of 175) |
Backbone | 93.6 % (902 of 964) | 93.4 % (312 of 334) | 93.9 % (443 of 472) | 93.0 % (147 of 158) |
Sidechain | 87.7 % (940 of 1072) | 87.4 % (562 of 643) | 91.0 % (375 of 412) | 17.6 % (3 of 17) |
Aromatic | 85.6 % (137 of 160) | 95.0 % (76 of 80) | 75.6 % (59 of 78) | 100.0 % (2 of 2) |
Methyl | 96.8 % (180 of 186) | 98.9 % (92 of 93) | 94.6 % (88 of 93) |
1. entity 1
GASNSEKTAL LTKTLNQGVK TIFDKLNERC IFYQAGFWIY EYCPGIEFVQ FHGRVNTKTG EIVNRDESLV YRLGKPKANV EEREFELLYD DVGYYISEII GSGDICDVTG AERMVEIQYV CGGSNSGPST IQWVRETKIC VYEAQVTIPE LCNLELLAKN EDSolvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.55 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 8.25 mM alpha3,alpha6-Man5, 95% H2O/5% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | MRH domain of Yos9 | [U-98% 13C; U-98% 15N] | 0.55 mM | |
2 | alpha3,alpha6-Man5 | natural abundance | 8.25 mM |
Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 1 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 15 mM alpha3,alpha6-Man5, 95% H2O/5% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
3 | MRH domain of Yos9 | [U-98% 13C; U-98% 15N] | 1 mM | |
4 | alpha3,alpha6-Man5 | natural abundance | 15 mM |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | internal | indirect | 0.1013291 |
Bruker Avance - 700 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 1 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 15 mM alpha3,alpha6-Man5, 95% H2O/5% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
3 | MRH domain of Yos9 | [U-98% 13C; U-98% 15N] | 1 mM | |
4 | alpha3,alpha6-Man5 | natural abundance | 15 mM |
Bruker Avance - 950 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.55 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 8.25 mM alpha3,alpha6-Man5, 95% H2O/5% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | MRH domain of Yos9 | [U-98% 13C; U-98% 15N] | 0.55 mM | |
2 | alpha3,alpha6-Man5 | natural abundance | 8.25 mM |
Bruker Avance - 700 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.55 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 8.25 mM alpha3,alpha6-Man5, 95% H2O/5% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | MRH domain of Yos9 | [U-98% 13C; U-98% 15N] | 0.55 mM | |
2 | alpha3,alpha6-Man5 | natural abundance | 8.25 mM |
Bruker Avance - 950 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.55 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 8.25 mM alpha3,alpha6-Man5, 95% H2O/5% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | MRH domain of Yos9 | [U-98% 13C; U-98% 15N] | 0.55 mM | |
2 | alpha3,alpha6-Man5 | natural abundance | 8.25 mM |
Bruker Avance - 950 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.55 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 8.25 mM alpha3,alpha6-Man5, 95% H2O/5% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | MRH domain of Yos9 | [U-98% 13C; U-98% 15N] | 0.55 mM | |
2 | alpha3,alpha6-Man5 | natural abundance | 8.25 mM |
Bruker Avance - 700 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.55 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 8.25 mM alpha3,alpha6-Man5, 95% H2O/5% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | MRH domain of Yos9 | [U-98% 13C; U-98% 15N] | 0.55 mM | |
2 | alpha3,alpha6-Man5 | natural abundance | 8.25 mM |
Bruker Avance - 700 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.55 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 8.25 mM alpha3,alpha6-Man5, 95% H2O/5% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | MRH domain of Yos9 | [U-98% 13C; U-98% 15N] | 0.55 mM | |
2 | alpha3,alpha6-Man5 | natural abundance | 8.25 mM |
Bruker Avance - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.55 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 8.25 mM alpha3,alpha6-Man5, 95% H2O/5% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | MRH domain of Yos9 | [U-98% 13C; U-98% 15N] | 0.55 mM | |
2 | alpha3,alpha6-Man5 | natural abundance | 8.25 mM |
Bruker Avance - 700 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.55 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 8.25 mM alpha3,alpha6-Man5, 95% H2O/5% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | MRH domain of Yos9 | [U-98% 13C; U-98% 15N] | 0.55 mM | |
2 | alpha3,alpha6-Man5 | natural abundance | 8.25 mM |
Bruker Avance - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.55 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 8.25 mM alpha3,alpha6-Man5, 95% H2O/5% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | MRH domain of Yos9 | [U-98% 13C; U-98% 15N] | 0.55 mM | |
2 | alpha3,alpha6-Man5 | natural abundance | 8.25 mM |
Bruker Avance - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.55 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 8.25 mM alpha3,alpha6-Man5, 95% H2O/5% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | MRH domain of Yos9 | [U-98% 13C; U-98% 15N] | 0.55 mM | |
2 | alpha3,alpha6-Man5 | natural abundance | 8.25 mM |
Bruker Avance - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.55 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 8.25 mM alpha3,alpha6-Man5, 95% H2O/5% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | MRH domain of Yos9 | [U-98% 13C; U-98% 15N] | 0.55 mM | |
2 | alpha3,alpha6-Man5 | natural abundance | 8.25 mM |
Bruker Avance - 700 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.55 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 8.25 mM alpha3,alpha6-Man5, 95% H2O/5% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | MRH domain of Yos9 | [U-98% 13C; U-98% 15N] | 0.55 mM | |
2 | alpha3,alpha6-Man5 | natural abundance | 8.25 mM |
Bruker Avance - 700 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.55 mM [U-98% 13C; U-98% 15N] MRH domain of Yos9, 8.25 mM alpha3,alpha6-Man5, 95% H2O/5% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | MRH domain of Yos9 | [U-98% 13C; U-98% 15N] | 0.55 mM | |
2 | alpha3,alpha6-Man5 | natural abundance | 8.25 mM |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_34219_6f9a.nef |
Input source #2: Coordindates | 6f9a.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 (Ã…) |
---|---|---|---|---|
A:117:CYS:SG | A:130:CYS:SG | oxidized, CA 56.52, CB 47.853 ppm | oxidized, CA 52.236, CB 44.093 ppm | 2.053 |
A:193:CYS:SG | A:227:CYS:SG | oxidized, CA 56.134, CB 43.625 ppm | oxidized, CA 56.757, CB 43.735 ppm | 2.011 |
A:208:CYS:SG | A:239:CYS:SG | oxidized, CA 55.84, CB 40.496 ppm | oxidized, CA 55.182, CB 39.632 ppm | 2.026 |
Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
NoneSequence alignments
--90------100-------110-------120-------130-------140-------150-------160-------170-------180------- GASNSEKTALLTKTLNQGVKTIFDKLNERCIFYQAGFWIYEYCPGIEFVQFHGRVNTKTGEIVNRDESLVYRLGKPKANVEEREFELLYDDVGYYISEII |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GASNSEKTALLTKTLNQGVKTIFDKLNERCIFYQAGFWIYEYCPGIEFVQFHGRVNTKTGEIVNRDESLVYRLGKPKANVEEREFELLYDDVGYYISEII --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 190-------200-------210-------220-------230-------240--------- GSGDICDVTGAERMVEIQYVCGGSNSGPSTIQWVRETKICVYEAQVTIPELCNLELLAKNED |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GSGDICDVTGAERMVEIQYVCGGSNSGPSTIQWVRETKICVYEAQVTIPELCNLELLAKNED -------110-------120-------130-------140-------150-------160--
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 162 | 0 | 0 | 100.0 |
Content subtype: combined_34219_6f9a.nef
Assigned chemical shifts
--90------100-------110-------120-------130-------140-------150-------160-------170-------180------- GASNSEKTALLTKTLNQGVKTIFDKLNERCIFYQAGFWIYEYCPGIEFVQFHGRVNTKTGEIVNRDESLVYRLGKPKANVEEREFELLYDDVGYYISEII ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| ....SEKTALLTKTLNQGVKTIFDKLNERCIFYQAGFWIYEYCPGIEFVQFHGRVNTKTGEIV...ESLVYRLGKPKANVEEREFELLYDDVGYYISEII 190-------200-------210-------220-------230-------240--------- GSGDICDVTGAERMVEIQYVCGGSNSGPSTIQWVRETKICVYEAQVTIPELCNLELLAKNED |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GSGDICDVTGAERMVEIQYVCGGSNSGPSTIQWVRETKICVYEAQVTIPELCNLELLAKNED
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 977 | 881 | 90.2 |
13C chemical shifts | 736 | 676 | 91.8 |
15N chemical shifts | 182 | 148 | 81.3 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 334 | 313 | 93.7 |
13C chemical shifts | 324 | 301 | 92.9 |
15N chemical shifts | 158 | 146 | 92.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 643 | 568 | 88.3 |
13C chemical shifts | 412 | 375 | 91.0 |
15N chemical shifts | 24 | 2 | 8.3 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 94 | 93 | 98.9 |
13C chemical shifts | 94 | 89 | 94.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 80 | 76 | 95.0 |
13C chemical shifts | 78 | 59 | 75.6 |
15N chemical shifts | 2 | 2 | 100.0 |
Covalent bonds
Distance restraints
--90------100-------110-------120-------130-------140-------150-------160-------170-------180------- GASNSEKTALLTKTLNQGVKTIFDKLNERCIFYQAGFWIYEYCPGIEFVQFHGRVNTKTGEIVNRDESLVYRLGKPKANVEEREFELLYDDVGYYISEII ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| ....SEKTALLTKTLNQGVKTIFDKLNERCIFYQAGFWIYEYCPGIEFVQFHGRVNTKTGEIV...ESLVYRLGKPKANVEEREFELLYDDVGYYISEII 190-------200-------210-------220-------230-------240--------- GSGDICDVTGAERMVEIQYVCGGSNSGPSTIQWVRETKICVYEAQVTIPELCNLELLAKNED |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GSGDICDVTGAERMVEIQYVCGGSNSGPSTIQWVRETKICVYEAQVTIPELCNLELLAKNED
Dihedral angle restraints
--90------100-------110-------120-------130-------140-------150-------160-------170-------180------- GASNSEKTALLTKTLNQGVKTIFDKLNERCIFYQAGFWIYEYCPGIEFVQFHGRVNTKTGEIVNRDESLVYRLGKPKANVEEREFELLYDDVGYYISEII ||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| GASNSEKTALLTKTLNQGVKTIFDKLNERCIFYQAGFWIYEYC.GIEFVQFHGRVNTKTGEIVNRDESLVYRLGKPKANVEEREFELLYDDVGYYISEII 190-------200-------210-------220-------230-------240--------- GSGDICDVTGAERMVEIQYVCGGSNSGPSTIQWVRETKICVYEAQVTIPELCNLELLAKNED |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GSGDICDVTGAERMVEIQYVCGGSNSGPSTIQWVRETKICVYEAQVTIPELCNLELLAKNED