Structure and NMR assignments of lantibiotic NAI-107 in DPC micelles
Polymer type: polypeptide(L)
Total | 1H | 13C | |
---|---|---|---|
All | 76.1 % (89 of 117) | 95.5 % (63 of 66) | 51.0 % (26 of 51) |
Backbone | 63.8 % (44 of 69) | 93.5 % (29 of 31) | 39.5 % (15 of 38) |
Sidechain | 89.7 % (52 of 58) | 97.1 % (34 of 35) | 78.3 % (18 of 23) |
Aromatic | 80.0 % (8 of 10) | 80.0 % (4 of 5) | 80.0 % (4 of 5) |
Methyl | 100.0 % (10 of 10) | 100.0 % (5 of 5) | 100.0 % (5 of 5) |
1. entity 1
VXXXXLCXPG CTXXGGGXNC XFCXSolvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.1 K, pH 6.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | natural abundance | 3.5 mM | |
2 | dodecylphosphocholine-d38 | [U-2H] | 150 mM | |
3 | potassium phosphate | natural abundance | 10 mM | |
4 | TSP-d4 | 2,2,3,3-D | 0.02 mM |
Bruker DRX - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.1 K, pH 6.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | natural abundance | 3.5 mM | |
2 | dodecylphosphocholine-d38 | [U-2H] | 150 mM | |
3 | potassium phosphate | natural abundance | 10 mM | |
4 | TSP-d4 | 2,2,3,3-D | 0.02 mM |
Bruker Avance - 900 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.1 K, pH 6.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | natural abundance | 3.5 mM | |
2 | dodecylphosphocholine-d38 | [U-2H] | 150 mM | |
3 | potassium phosphate | natural abundance | 10 mM | |
4 | TSP-d4 | 2,2,3,3-D | 0.02 mM |
Bruker Avance - 900 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.1 K, pH 6.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | natural abundance | 3.5 mM | |
2 | dodecylphosphocholine-d38 | [U-2H] | 150 mM | |
3 | potassium phosphate | natural abundance | 10 mM | |
4 | TSP-d4 | 2,2,3,3-D | 0.02 mM |
Bruker Avance - 900 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.1 K, pH 6.2
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | natural abundance | 3.5 mM | |
2 | dodecylphosphocholine-d38 | [U-2H] | 150 mM | |
3 | potassium phosphate | natural abundance | 10 mM | |
4 | TSP-d4 | 2,2,3,3-D | 0.02 mM |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_19619_2mh5.nef |
Input source #2: Coordindates | 2mh5.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 | Error |
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) |
---|---|---|---|---|
1:1:VAL:C | 1:2:DBU:N | unknown | unknown | n/a |
1:2:DBU:C | 1:3:DAL:N | unknown | unknown | n/a |
1:3:DAL:C | 1:4:5CW:N | unknown | unknown | n/a |
1:4:5CW:C | 1:5:DHA:N | unknown | unknown | n/a |
1:5:DHA:C | 1:6:LEU:N | unknown | unknown | n/a |
1:12:THR:C | 1:13:DAL:N | unknown | unknown | n/a |
1:17:GLY:C | 1:18:DAL:N | unknown | unknown | n/a |
1:18:DAL:C | 1:19:ASN:N | unknown | unknown | n/a |
1:20:CYS:C | 1:21:DAL:N | unknown | unknown | n/a |
1:21:DAL:C | 1:22:PHE:N | unknown | unknown | n/a |
1:18:DAL:CB | 1:23:CYS:SG | unknown | unknown | n/a |
1:13:DAL:CB | 1:20:CYS:SG | unknown | unknown | n/a |
1:21:DAL:CB | 1:24:TEE:SG | unknown | unknown | n/a |
1:3:DAL:CB | 1:7:CYS:SG | unknown | unknown | n/a |
1:8:DBB:CB | 1:11:CYS:SG | unknown | unknown | n/a |
1:8:DBB:C | 1:9:PRO:N | unknown | unknown | n/a |
1:13:DAL:C | 1:14:HYP:N | unknown | unknown | n/a |
1:14:HYP:C | 1:15:GLY:N | unknown | unknown | n/a |
1:7:CYS:C | 1:8:DBB:N | unknown | unknown | n/a |
1:23:CYS:C | 1:24:TEE:N | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
A | 2 | DBU | (2Z)-2-AMINOBUT-2-ENOIC ACID | Assigned chemical shifts, Torsion angle restraints, Coordinates |
A | 3 | DAL | D-ALANINE | Assigned chemical shifts, Coordinates |
A | 4 | 5CW | 5-chloro-L-tryptophan | Assigned chemical shifts, Coordinates |
A | 5 | DHA | 2-AMINO-ACRYLIC ACID | Assigned chemical shifts, Torsion angle restraints, Coordinates |
A | 8 | DBB | D-ALPHA-AMINOBUTYRIC ACID | Assigned chemical shifts, Coordinates |
A | 13 | DAL | D-ALANINE | Assigned chemical shifts, Torsion angle restraints, Coordinates |
A | 14 | HYP | 4-HYDROXYPROLINE | Assigned chemical shifts, Torsion angle restraints, Coordinates |
A | 18 | DAL | D-ALANINE | Assigned chemical shifts, Torsion angle restraints, Coordinates |
A | 21 | DAL | D-ALANINE | Assigned chemical shifts, Coordinates |
A | 24 | TEE | 2-AMINO-ETHENETHIOL | Assigned chemical shifts, Coordinates |
B | 1 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 2 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 3 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 4 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 5 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 6 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 7 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 8 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 9 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 10 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 11 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 12 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 13 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 14 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 15 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 16 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 17 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 18 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 19 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 20 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 21 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 22 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 23 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 24 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 25 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 26 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 27 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 28 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 29 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 30 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 31 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 32 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 33 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 34 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 35 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 36 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 37 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 38 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 39 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 40 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 41 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 42 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 43 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 44 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 45 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 46 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 47 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 48 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 49 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 50 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 51 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 52 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 53 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 54 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 55 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 56 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 57 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 58 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 59 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 60 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 61 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 62 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 63 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 64 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
B | 65 | DPV | dodecyl 2-(trimethylammonio)ethyl phosphate | None |
Sequence alignments
--------10--------20---- VXXXXLCXPGCTXXGGGXNCXFCX |||||||||||||||||||||||| VXXXXLCXPGCTXXGGGXNCXFCX
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 24 | 0 | 0 | 100.0 |
Content subtype: combined_19619_2mh5.nef
Assigned chemical shifts
Comp_index_ID | Comp_ID |
---|---|
4 | 5CW |
8 | DBB |
24 | TEE |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 91 | 80 | 87.9 |
13C chemical shifts | 71 | 30 | 42.3 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 42 | 38 | 90.5 |
13C chemical shifts | 38 | 9 | 23.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 49 | 42 | 85.7 |
13C chemical shifts | 33 | 21 | 63.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 10 | 7 | 70.0 |
13C chemical shifts | 10 | 6 | 60.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 5 | 4 | 80.0 |
13C chemical shifts | 5 | 4 | 80.0 |
Covalent bonds
Distance restraints
Dihedral angle restraints
--------10--------20---- VXXXXLCXPGCTXXGGGXNCXFCX || ||| ||||||||||| VX..XLC.PGCTXXGGGXN --------10---------