NMR solution structure of vicilin-buried peptide-8 (VBP-8)
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | disulfide | sing | 1:CYS13:SG | 1:CYS33:SG |
2 | disulfide | sing | 1:CYS17:SG | 1:CYS29:SG |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 75.6 % (455 of 602) | 92.5 % (309 of 334) | 48.3 % (99 of 205) | 74.6 % (47 of 63) |
Backbone | 76.7 % (224 of 292) | 99.0 % (100 of 101) | 54.5 % (78 of 143) | 95.8 % (46 of 48) |
Sidechain | 72.4 % (257 of 355) | 90.1 % (210 of 233) | 43.0 % (46 of 107) | 6.7 % (1 of 15) |
Aromatic | 50.0 % (10 of 20) | 100.0 % (10 of 10) | 0.0 % (0 of 10) | |
Methyl | 70.0 % (7 of 10) | 100.0 % (5 of 5) | 40.0 % (2 of 5) |
1. entity 1
RGPDKSYKRL QECQRRCQSE QQGQRLQECQ QRCQQEYQRE KGQHQGETNSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4 (±0.2), Details 2 mg/mL VBP-8, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VBP-8 | natural abundance | 2 mg/mL |
Bruker Avance III - 700 MHz equipped with cryoprobe
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4 (±0.2), Details 2 mg/mL VBP-8, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VBP-8 | natural abundance | 2 mg/mL |
Bruker Avance III - 700 MHz equipped with cryoprobe
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4 (±0.2), Details 2 mg/mL VBP-8, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VBP-8 | natural abundance | 2 mg/mL |
Bruker Avance III - 700 MHz equipped with cryoprobe
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4 (±0.2), Details 2 mg/mL VBP-8, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VBP-8 | natural abundance | 2 mg/mL |
Bruker Avance III - 700 MHz equipped with cryoprobe
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4 (±0.2), Details 2 mg/mL VBP-8, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VBP-8 | natural abundance | 2 mg/mL |
Bruker Avance III - 700 MHz equipped with cryoprobe
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 4 (±0.2), Details 2 mg/mL VBP-8, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VBP-8 | natural abundance | 2 mg/mL |
Bruker Avance III - 700 MHz equipped with cryoprobe
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 4 (±0.2), Details 2 mg/mL VBP-8, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VBP-8 | natural abundance | 2 mg/mL |
Bruker Avance III - 700 MHz equipped with cryoprobe
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 4 (±0.2), Details 2 mg/mL VBP-8, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VBP-8 | natural abundance | 2 mg/mL |
Bruker Avance III - 700 MHz equipped with cryoprobe
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 4 (±0.2), Details 2 mg/mL VBP-8, 90% H2O/10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | VBP-8 | natural abundance | 2 mg/mL |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_30579_6o3q.nef |
Input source #2: Coordindates | 6o3q.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:13:CYS:SG | A:33:CYS:SG | oxidized, CA 58.805, CB 36.399 ppm | oxidized, CA 56.914, CB 36.769 ppm | 2.022 |
A:17:CYS:SG | A:29:CYS:SG | oxidized, CA 56.951, CB 37.051 ppm | oxidized, CA 60.551, CB 35.83 ppm | 2.033 |
Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
NoneSequence alignments
--------10--------20--------30--------40--------- RGPDKSYKRLQECQRRCQSEQQGQRLQECQQRCQQEYQREKGQHQGETN ||||||||||||||||||||||||||||||||||||||||||||||||| RGPDKSYKRLQECQRRCQSEQQGQRLQECQQRCQQEYQREKGQHQGETN
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 49 | 0 | 0 | 100.0 |
Content subtype: combined_30579_6o3q.nef
Assigned chemical shifts
--------10--------20--------30--------40--------- RGPDKSYKRLQECQRRCQSEQQGQRLQECQQRCQQEYQREKGQHQGETN ||||||||||||||||||||||||||||||||||||||||||||||||| RGPDKSYKRLQECQRRCQSEQQGQRLQECQQRCQQEYQREKGQHQGETN
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 334 | 306 | 91.6 |
13C chemical shifts | 205 | 90 | 43.9 |
15N chemical shifts | 70 | 46 | 65.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 101 | 100 | 99.0 |
13C chemical shifts | 98 | 49 | 50.0 |
15N chemical shifts | 48 | 46 | 95.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 233 | 206 | 88.4 |
13C chemical shifts | 107 | 41 | 38.3 |
15N chemical shifts | 22 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 5 | 5 | 100.0 |
13C chemical shifts | 5 | 2 | 40.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 10 | 10 | 100.0 |
13C chemical shifts | 10 | 0 | 0.0 |
Covalent bonds
Distance restraints
--------10--------20--------30--------40--------- RGPDKSYKRLQECQRRCQSEQQGQRLQECQQRCQQEYQREKGQHQGETN ||||||||||||||||||||||||||||||||||||||||||||||||| RGPDKSYKRLQECQRRCQSEQQGQRLQECQQRCQQEYQREKGQHQGETN
--------10--------20--------30--------40--------- RGPDKSYKRLQECQRRCQSEQQGQRLQECQQRCQQEYQREKGQHQGETN ||||||||||||||| |||| |||||||||| || | ...DKSYKRLQECQRRCQ.EQQG.RLQECQQRCQ.EY..E --------10--------20--------30--------40
Dihedral angle restraints
--------10--------20--------30--------40--------- RGPDKSYKRLQECQRRCQSEQQGQRLQECQQRCQQEYQREKGQHQGETN |||||||||||||||||||||||||||||||||||||||| ..PDKSYKRLQECQRRCQSEQQGQRLQECQQRCQQEYQREKG --------10--------20--------30--------40--