Solution structure of a zinc-binding methionine sulfoxide reductase
GSHMKDRIPI FSVAKNRVEM VERIELSDDE WREILDPEAF RVARKAGTEP PFTGKYHDLH DDGIYRCICC GTDLFDSETK FDSGTGWPSF YDVVSEHNIK LREDRSLGMV RCEVLCARCD AHLGHVFDDG PRPTGKRYCM NSAALKFIPR DQIG
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 87.8 % (1555 of 1771) | 89.4 % (827 of 925) | 84.7 % (588 of 694) | 92.1 % (140 of 152) |
Backbone | 91.6 % (832 of 908) | 94.9 % (296 of 312) | 89.1 % (401 of 450) | 92.5 % (135 of 146) |
Sidechain | 85.0 % (854 of 1005) | 86.8 % (532 of 613) | 82.1 % (317 of 386) | 83.3 % (5 of 6) |
Aromatic | 58.7 % (94 of 160) | 66.3 % (53 of 80) | 51.3 % (40 of 78) | 50.0 % (1 of 2) |
Methyl | 96.3 % (131 of 136) | 97.1 % (66 of 68) | 95.6 % (65 of 68) |
1. msrb
GSHMKDRIPI FSVAKNRVEM VERIELSDDE WREILDPEAF RVARKAGTEP PFTGKYHDLH DDGIYRCICC GTDLFDSETK FDSGTGWPSF YDVVSEHNIK LREDRSLGMV RCEVLCARCD AHLGHVFDDG PRPTGKRYCM NSAALKFIPR DQIGSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | msrb | [U-15N] | 1.2 mM | |
2 | Na-phosphate | natural abundance | 20 mM | |
3 | NaCl | natural abundance | 20 mM | |
4 | beta-mercaptoethanol | natural abundance | 5 mM |
Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
5 | msrb | [U-13C; U-15N] | 1.2 mM | |
6 | Na-phosphate | natural abundance | 20 mM | |
7 | NaCl | natural abundance | 20 mM | |
8 | beta-mercaptoethanol | natural abundance | 5 mM |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | dioxane | carbon | 67.83 ppm | internal | direct | 1.0 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | [15N] ammonium chloride | nitrogen | 24.93 ppm | internal | direct | 1.0 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | dioxane | carbon | 67.83 ppm | internal | direct | 1.0 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | [15N] ammonium chloride | nitrogen | 24.93 ppm | internal | direct | 1.0 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | dioxane | carbon | 67.83 ppm | internal | direct | 1.0 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | [15N] ammonium chloride | nitrogen | 24.93 ppm | internal | direct | 1.0 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | dioxane | carbon | 67.83 ppm | internal | direct | 1.0 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | [15N] ammonium chloride | nitrogen | 24.93 ppm | internal | direct | 1.0 |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | msrb | [U-15N] | 1.2 mM | |
2 | Na-phosphate | natural abundance | 20 mM | |
3 | NaCl | natural abundance | 20 mM | |
4 | beta-mercaptoethanol | natural abundance | 5 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
5 | msrb | [U-13C; U-15N] | 1.2 mM | |
6 | Na-phosphate | natural abundance | 20 mM | |
7 | NaCl | natural abundance | 20 mM | |
8 | beta-mercaptoethanol | natural abundance | 5 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
5 | msrb | [U-13C; U-15N] | 1.2 mM | |
6 | Na-phosphate | natural abundance | 20 mM | |
7 | NaCl | natural abundance | 20 mM | |
8 | beta-mercaptoethanol | natural abundance | 5 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
5 | msrb | [U-13C; U-15N] | 1.2 mM | |
6 | Na-phosphate | natural abundance | 20 mM | |
7 | NaCl | natural abundance | 20 mM | |
8 | beta-mercaptoethanol | natural abundance | 5 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | msrb | [U-15N] | 1.2 mM | |
2 | Na-phosphate | natural abundance | 20 mM | |
3 | NaCl | natural abundance | 20 mM | |
4 | beta-mercaptoethanol | natural abundance | 5 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
5 | msrb | [U-13C; U-15N] | 1.2 mM | |
6 | Na-phosphate | natural abundance | 20 mM | |
7 | NaCl | natural abundance | 20 mM | |
8 | beta-mercaptoethanol | natural abundance | 5 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
5 | msrb | [U-13C; U-15N] | 1.2 mM | |
6 | Na-phosphate | natural abundance | 20 mM | |
7 | NaCl | natural abundance | 20 mM | |
8 | beta-mercaptoethanol | natural abundance | 5 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | msrb | [U-15N] | 1.2 mM | |
2 | Na-phosphate | natural abundance | 20 mM | |
3 | NaCl | natural abundance | 20 mM | |
4 | beta-mercaptoethanol | natural abundance | 5 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
5 | msrb | [U-13C; U-15N] | 1.2 mM | |
6 | Na-phosphate | natural abundance | 20 mM | |
7 | NaCl | natural abundance | 20 mM | |
8 | beta-mercaptoethanol | natural abundance | 5 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
5 | msrb | [U-13C; U-15N] | 1.2 mM | |
6 | Na-phosphate | natural abundance | 20 mM | |
7 | NaCl | natural abundance | 20 mM | |
8 | beta-mercaptoethanol | natural abundance | 5 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
5 | msrb | [U-13C; U-15N] | 1.2 mM | |
6 | Na-phosphate | natural abundance | 20 mM | |
7 | NaCl | natural abundance | 20 mM | |
8 | beta-mercaptoethanol | natural abundance | 5 mM |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints | combined_15941_2k8d.nef |
Input source #2: Coordindates | 2k8d.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 | True (see coodinates for details) |
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)
Ptnr_site_1 | Ptnr_site_2 | Redox_state_prediction_1 | Redox_state_prediction_2 | Distance (Å) |
---|---|---|---|---|
1:64:CYS:SG | 2:1:ZN:ZN | unknown | unknown | n/a |
1:67:CYS:SG | 2:1:ZN:ZN | unknown | unknown | n/a |
1:113:CYS:SG | 2:1:ZN:ZN | unknown | unknown | n/a |
1:116:CYS:SG | 2:1:ZN:ZN | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 1 | ZN | ZINC ION | None |
Sequence alignments
-----10--------20--------30--------40--------50--------60--------70--------80--------90-------100--- MKDRIPIFSVAKNRVEMVERIELSDDEWREILDPEAFRVARKAGTEPPFTGKYHDLHDDGIYRCICCGTDLFDSETKFDSGTGWPSFYDVVSEHNIKLRE |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MKDRIPIFSVAKNRVEMVERIELSDDEWREILDPEAFRVARKAGTEPPFTGKYHDLHDDGIYRCICCGTDLFDSETKFDSGTGWPSFYDVVSEHNIKLRE --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 ----110-------120-------130-------140-------150---- DRSLGMVRCEVLCARCDAHLGHVFDDGPRPTGKRYCMNSAALKFIPRDQIG ||||||||||||||||||||||||||||||||||||||||||||||||||| DRSLGMVRCEVLCARCDAHLGHVFDDGPRPTGKRYCMNSAALKFIPRDQIG -------110-------120-------130-------140-------150-
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 151 | 0 | 0 | 100.0 |
Content subtype: combined_15941_2k8d.nef
Assigned chemical shifts
-----10--------20--------30--------40--------50--------60--------70--------80--------90-------100--- MKDRIPIFSVAKNRVEMVERIELSDDEWREILDPEAFRVARKAGTEPPFTGKYHDLHDDGIYRCICCGTDLFDSETKFDSGTGWPSFYDVVSEHNIKLRE ||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||| |||||||||||||||||||| .KDRIPIFSVAKNRVEMVERIELSDDEWREILDPEAFRVARKAGTE...TG......DDGIYRCICCGTDLFDSETKFD.GTGWPSFYDVVSEHNIKLRE ----110-------120-------130-------140-------150---- DRSLGMVRCEVLCARCDAHLGHVFDDGPRPTGKRYCMNSAALKFIPRDQIG ||||||||||||||||||||||||||| |||||||||||||||||||||| DRSLGMVRCEVLCARCDAHLGHVFDDG..PTGKRYCMNSAALKFIPRDQIG
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 912 | 770 | 84.4 |
13C chemical shifts | 684 | 556 | 81.3 |
15N chemical shifts | 163 | 134 | 82.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 305 | 278 | 91.1 |
13C chemical shifts | 302 | 254 | 84.1 |
15N chemical shifts | 143 | 129 | 90.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 607 | 492 | 81.1 |
13C chemical shifts | 382 | 302 | 79.1 |
15N chemical shifts | 20 | 5 | 25.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 72 | 67 | 93.1 |
13C chemical shifts | 72 | 66 | 91.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 78 | 37 | 47.4 |
13C chemical shifts | 76 | 36 | 47.4 |
15N chemical shifts | 2 | 1 | 50.0 |
Covalent bonds
Distance restraints
-----10--------20--------30--------40--------50--------60--------70--------80--------90-------100--- MKDRIPIFSVAKNRVEMVERIELSDDEWREILDPEAFRVARKAGTEPPFTGKYHDLHDDGIYRCICCGTDLFDSETKFDSGTGWPSFYDVVSEHNIKLRE |||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| ||||||||||||||||||| ..DRIPIFSVAKNRVEMVERIELSDDEWREILDPEAFRVARKAGTE...........DDGIYRCICCGTDLFDSETKFD..TGWPSFYDVVSEHNIKLRE ----110-------120-------130-------140-------150---- DRSLGMVRCEVLCARCDAHLGHVFDDGPRPTGKRYCMNSAALKFIPRDQIG ||||||||||||||||||||||||||| |||||||||||||||||||||| DRSLGMVRCEVLCARCDAHLGHVFDDG..PTGKRYCMNSAALKFIPRDQIG