NMR structure of N-terminal domain from A. ventricosus minor ampullate spidroin (MiSp) at pH 5.5
GSGNSQPIWT NPNAAMTMTN NLVQCASRSG VLTADQMDDM GMMADSVNSQ MQKMGPNPPQ HRLRAMNTAM AAEVAEVVAT SPPQSYSAVL NTIGACLRES MMQATGSVDN AFTNEVMQLV KMLSADSANE VST
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | disulfide | sing | 1:CYS25:SG | 1:CYS96:SG |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 93.9 % (1327 of 1413) | 96.7 % (704 of 728) | 89.4 % (480 of 537) | 96.6 % (143 of 148) |
Backbone | 91.3 % (716 of 784) | 96.2 % (256 of 266) | 86.0 % (337 of 392) | 97.6 % (123 of 126) |
Sidechain | 97.4 % (735 of 755) | 97.0 % (448 of 462) | 98.5 % (267 of 271) | 90.9 % (20 of 22) |
Aromatic | 97.1 % (33 of 34) | 100.0 % (17 of 17) | 100.0 % (16 of 16) | 0.0 % (0 of 1) |
Methyl | 97.8 % (131 of 134) | 97.0 % (65 of 67) | 98.5 % (66 of 67) |
1. entity
GSGNSQPIWT NPNAAMTMTN NLVQCASRSG VLTADQMDDM GMMADSVNSQ MQKMGPNPPQ HRLRAMNTAM AAEVAEVVAT SPPQSYSAVL NTIGACLRES MMQATGSVDN AFTNEVMQLV KMLSADSANE VSTSolvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 295 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-99% 13C; U-99% 15N] | 0.5 mM | |
2 | sodium chloride | natural abundance | 20 mM | |
3 | sodium azide | natural abundance | 0.03 % | |
4 | sodium acetate | [U-99% 2H] | 20 mM | |
5 | protease inhibitor cocktail | natural abundance | 0.01 tablet/100mL |
Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 295 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | entity | [U-99% 13C; U-99% 15N] | 11.3 mg/mL | |
7 | entity | natural abundance | 11.3 mg/mL | |
8 | sodium chloride | natural abundance | 20 mM | |
9 | sodium azide | natural abundance | 0.03 % | |
10 | sodium acetate | [U-2H] | 20 mM | |
11 | protease inhibitor cocktail | natural abundance | 0.01 tablet/100mL |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | water | protons | 4.8 ppm | internal | indirect | 0.2514495 |
1H | water | protons | 4.8 ppm | internal | indirect | 1.0 |
15N | water | protons | 4.8 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | water | protons | 4.8 ppm | internal | indirect | 0.2514495 |
1H | water | protons | 4.8 ppm | internal | indirect | 1.0 |
15N | water | protons | 4.8 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | water | protons | 4.8 ppm | internal | indirect | 0.2514495 |
1H | water | protons | 4.8 ppm | internal | indirect | 1.0 |
15N | water | protons | 4.8 ppm | internal | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | water | protons | 4.8 ppm | internal | indirect | 0.2514495 |
1H | water | protons | 4.8 ppm | internal | indirect | 1.0 |
15N | water | protons | 4.8 ppm | internal | indirect | 0.1013291 |
Varian INOVA - 600 MHz equipped with HCN cold probe
State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 295 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-99% 13C; U-99% 15N] | 0.5 mM | |
2 | sodium chloride | natural abundance | 20 mM | |
3 | sodium azide | natural abundance | 0.03 % | |
4 | sodium acetate | [U-99% 2H] | 20 mM | |
5 | protease inhibitor cocktail | natural abundance | 0.01 tablet/100mL |
Varian INOVA - 600 MHz equipped with HCN cold probe
State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 295 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-99% 13C; U-99% 15N] | 0.5 mM | |
2 | sodium chloride | natural abundance | 20 mM | |
3 | sodium azide | natural abundance | 0.03 % | |
4 | sodium acetate | [U-99% 2H] | 20 mM | |
5 | protease inhibitor cocktail | natural abundance | 0.01 tablet/100mL |
Varian INOVA - 600 MHz equipped with HCN cold probe
State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 295 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-99% 13C; U-99% 15N] | 0.5 mM | |
2 | sodium chloride | natural abundance | 20 mM | |
3 | sodium azide | natural abundance | 0.03 % | |
4 | sodium acetate | [U-99% 2H] | 20 mM | |
5 | protease inhibitor cocktail | natural abundance | 0.01 tablet/100mL |
Varian INOVA - 600 MHz equipped with HCN cold probe
State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 295 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-99% 13C; U-99% 15N] | 0.5 mM | |
2 | sodium chloride | natural abundance | 20 mM | |
3 | sodium azide | natural abundance | 0.03 % | |
4 | sodium acetate | [U-99% 2H] | 20 mM | |
5 | protease inhibitor cocktail | natural abundance | 0.01 tablet/100mL |
Varian INOVA - 600 MHz equipped with HCN cold probe
State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 295 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-99% 13C; U-99% 15N] | 0.5 mM | |
2 | sodium chloride | natural abundance | 20 mM | |
3 | sodium azide | natural abundance | 0.03 % | |
4 | sodium acetate | [U-99% 2H] | 20 mM | |
5 | protease inhibitor cocktail | natural abundance | 0.01 tablet/100mL |
Varian INOVA - 600 MHz equipped with HCN cold probe
State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 295 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-99% 13C; U-99% 15N] | 0.5 mM | |
2 | sodium chloride | natural abundance | 20 mM | |
3 | sodium azide | natural abundance | 0.03 % | |
4 | sodium acetate | [U-99% 2H] | 20 mM | |
5 | protease inhibitor cocktail | natural abundance | 0.01 tablet/100mL |
Varian INOVA - 600 MHz equipped with HCN cold probe
State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 295 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-99% 13C; U-99% 15N] | 0.5 mM | |
2 | sodium chloride | natural abundance | 20 mM | |
3 | sodium azide | natural abundance | 0.03 % | |
4 | sodium acetate | [U-99% 2H] | 20 mM | |
5 | protease inhibitor cocktail | natural abundance | 0.01 tablet/100mL |
Varian INOVA - 600 MHz equipped with HCN cold probe
State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 295 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity | [U-99% 13C; U-99% 15N] | 0.5 mM | |
2 | sodium chloride | natural abundance | 20 mM | |
3 | sodium azide | natural abundance | 0.03 % | |
4 | sodium acetate | [U-99% 2H] | 20 mM | |
5 | protease inhibitor cocktail | natural abundance | 0.01 tablet/100mL |
Varian INOVA - 600 MHz equipped with HCN cold probe
State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 295 K, pH 5.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | entity | [U-99% 13C; U-99% 15N] | 11.3 mg/mL | |
7 | entity | natural abundance | 11.3 mg/mL | |
8 | sodium chloride | natural abundance | 20 mM | |
9 | sodium azide | natural abundance | 0.03 % | |
10 | sodium acetate | [U-2H] | 20 mM | |
11 | protease inhibitor cocktail | natural abundance | 0.01 tablet/100mL |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints | combined_25398_2mx9.nef |
Input source #2: Coordindates | 2mx9.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:25:CYS:SG | A:96:CYS:SG | oxidized, CA 59.813, CB 36.59 ppm | oxidized, CA 56.086, CB 37.388 ppm | 2.029 |
B:25:CYS:SG | B:96:CYS:SG | unknown | unknown | 2.032 |
Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
NoneSequence alignments
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GSGNSQPIWTNPNAAMTMTNNLVQCASRSGVLTADQMDDMGMMADSVNSQMQKMGPNPPQHRLRAMNTAMAAEVAEVVATSPPQSYSAVLNTIGACLRES |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GSGNSQPIWTNPNAAMTMTNNLVQCASRSGVLTADQMDDMGMMADSVNSQMQKMGPNPPQHRLRAMNTAMAAEVAEVVATSPPQSYSAVLNTIGACLRES -------110-------120-------130--- MMQATGSVDNAFTNEVMQLVKMLSADSANEVST ||||||||||||||||||||||||||||||||| MMQATGSVDNAFTNEVMQLVKMLSADSANEVST
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GSGNSQPIWTNPNAAMTMTNNLVQCASRSGVLTADQMDDMGMMADSVNSQMQKMGPNPPQHRLRAMNTAMAAEVAEVVATSPPQSYSAVLNTIGACLRES |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GSGNSQPIWTNPNAAMTMTNNLVQCASRSGVLTADQMDDMGMMADSVNSQMQKMGPNPPQHRLRAMNTAMAAEVAEVVATSPPQSYSAVLNTIGACLRES -------110-------120-------130--- MMQATGSVDNAFTNEVMQLVKMLSADSANEVST ||||||||||||||||||||||||||||||||| MMQATGSVDNAFTNEVMQLVKMLSADSANEVST
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 133 | 0 | 0 | 100.0 |
B | B | 133 | 0 | 0 | 100.0 |
Content subtype: combined_25398_2mx9.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GSGNSQPIWTNPNAAMTMTNNLVQCASRSGVLTADQMDDMGMMADSVNSQMQKMGPNPPQHRLRAMNTAMAAEVAEVVATSPPQSYSAVLNTIGACLRES |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ..GNSQPIWTNPNAAMTMTNNLVQCASRSGVLTADQMDDMGMMADSVNSQMQKMGPNPPQHRLRAMNTAMAAEVAEVVATSPPQSYSAVLNTIGACLRES -------110-------120-------130--- MMQATGSVDNAFTNEVMQLVKMLSADSANEVST ||||||||||||||||||||||||||||||||| MMQATGSVDNAFTNEVMQLVKMLSADSANEVST
Comp_index_ID | Comp_ID | Atom_ID | CS value (ppm) |
---|---|---|---|
19 | THR | HG1 | 4.355 |
29 | SER | HG | 5.482 |
81 | SER | HG | 5.716 |
92 | THR | HG1 | 5.119 |
100 | SER | HG | 4.61 |
113 | THR | HG1 | 4.866 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 728 | 712 | 97.8 |
13C chemical shifts | 537 | 469 | 87.3 |
15N chemical shifts | 152 | 145 | 95.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 266 | 259 | 97.4 |
13C chemical shifts | 266 | 202 | 75.9 |
15N chemical shifts | 126 | 122 | 96.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 462 | 453 | 98.1 |
13C chemical shifts | 271 | 267 | 98.5 |
15N chemical shifts | 26 | 23 | 88.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 81 | 80 | 98.8 |
13C chemical shifts | 81 | 80 | 98.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 17 | 17 | 100.0 |
13C chemical shifts | 16 | 16 | 100.0 |
15N chemical shifts | 1 | 0 | 0.0 |
Covalent bonds
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GSGNSQPIWTNPNAAMTMTNNLVQCASRSGVLTADQMDDMGMMADSVNSQMQKMGPNPPQHRLRAMNTAMAAEVAEVVATSPPQSYSAVLNTIGACLRES ||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ..GNSQPIW.NPNAAMTMTNNLVQCASRSGVLTADQMDDMGMMADSVNSQMQKMGPNPPQHRLRAMNTAMAAEVAEVVATSPPQSYSAVLNTIGACLRES -------110-------120-------130--- MMQATGSVDNAFTNEVMQLVKMLSADSANEVST ||||||||||||||||||||||||||||||||| MMQATGSVDNAFTNEVMQLVKMLSADSANEVST
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GSGNSQPIWTNPNAAMTMTNNLVQCASRSGVLTADQMDDMGMMADSVNSQMQKMGPNPPQHRLRAMNTAMAAEVAEVVATSPPQSYSAVLNTIGACLRES ||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ..GNSQPIW.NPNAAMTMTNNLVQCASRSGVLTADQMDDMGMMADSVNSQMQKMGPNPPQHRLRAMNTAMAAEVAEVVATSPPQSYSAVLNTIGACLRES -------110-------120-------130--- MMQATGSVDNAFTNEVMQLVKMLSADSANEVST ||||||||||||||||||||||||||||||||| MMQATGSVDNAFTNEVMQLVKMLSADSANEVST