NMR solution structure of chitin-binding domain from dust mite group XII allergen Blo t 12.
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | disulfide | sing | 1:CYS20:SG | 1:CYS38:SG |
2 | disulfide | sing | 1:CYS52:SG | 1:CYS65:SG |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 97.0 % (756 of 779) | 98.3 % (395 of 402) | 95.2 % (295 of 310) | 98.5 % (66 of 67) |
Backbone | 97.8 % (393 of 402) | 99.3 % (139 of 140) | 96.5 % (192 of 199) | 98.4 % (62 of 63) |
Sidechain | 96.8 % (424 of 438) | 97.7 % (256 of 262) | 95.3 % (164 of 172) | 100.0 % (4 of 4) |
Aromatic | 78.8 % (52 of 66) | 81.8 % (27 of 33) | 75.0 % (24 of 32) | 100.0 % (1 of 1) |
Methyl | 100.0 % (74 of 74) | 100.0 % (37 of 37) | 100.0 % (37 of 37) |
1. entity
GPLGSDLIVH EGGKTYHVVC HEEGPIPHPG NVHKYIICSK SGSLWYITVM PCSIGTKFDP ISRNCVLDNSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.1) K, pH 6.0 (±0.1), Details 13C, 15N Blo t 12 CBD
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Blo t 12 CBD | [U-100% 13C; U-100% 15N] | 1 (±0.05) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±1.0) mM | |
4 | H2O | natural abundance | 90 (±1.0) % | |
5 | D2O | natural abundance | 10 (±1.0) % |
Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.1) K, pH 6.0 (±0.1), Details 15N Blo t 12 CBD
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | Blo t 12 CBD | [U-100% 15N] | 1 (±0.05) mM | |
7 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
8 | sodium chloride | natural abundance | 100 (±1.0) mM | |
9 | H2O | natural abundance | 90 (±1.0) % | |
10 | D2O | natural abundance | 10 (±1.0) % |
Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.1) K, pH 6.0 (±0.1), Details 15N Blo t 12 CBD in Pf1 phage alignment medium.
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
11 | Blo t 12 CBD | [U-100% 15N] | 1 (±0.05) mM | |
12 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
13 | sodium chloride | natural abundance | 100 (±1.0) mM | |
14 | Pf1 phage | natural abundance | 11 (±0.1) mg/mL | |
15 | H2O | natural abundance | 90 (±0.1) % | |
16 | D2O | natural abundance | 10 (±0.1) % |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.1) K, pH 6.0 (±0.1), Details 15N Blo t 12 CBD
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | Blo t 12 CBD | [U-100% 15N] | 1 (±0.05) mM | |
7 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
8 | sodium chloride | natural abundance | 100 (±1.0) mM | |
9 | H2O | natural abundance | 90 (±1.0) % | |
10 | D2O | natural abundance | 10 (±1.0) % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.1) K, pH 6.0 (±0.1), Details 13C, 15N Blo t 12 CBD
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Blo t 12 CBD | [U-100% 13C; U-100% 15N] | 1 (±0.05) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±1.0) mM | |
4 | H2O | natural abundance | 90 (±1.0) % | |
5 | D2O | natural abundance | 10 (±1.0) % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.1) K, pH 6.0 (±0.1), Details 13C, 15N Blo t 12 CBD
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Blo t 12 CBD | [U-100% 13C; U-100% 15N] | 1 (±0.05) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±1.0) mM | |
4 | H2O | natural abundance | 90 (±1.0) % | |
5 | D2O | natural abundance | 10 (±1.0) % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.1) K, pH 6.0 (±0.1), Details 13C, 15N Blo t 12 CBD
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Blo t 12 CBD | [U-100% 13C; U-100% 15N] | 1 (±0.05) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±1.0) mM | |
4 | H2O | natural abundance | 90 (±1.0) % | |
5 | D2O | natural abundance | 10 (±1.0) % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.1) K, pH 6.0 (±0.1), Details 13C, 15N Blo t 12 CBD
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Blo t 12 CBD | [U-100% 13C; U-100% 15N] | 1 (±0.05) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±1.0) mM | |
4 | H2O | natural abundance | 90 (±1.0) % | |
5 | D2O | natural abundance | 10 (±1.0) % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.1) K, pH 6.0 (±0.1), Details 13C, 15N Blo t 12 CBD
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Blo t 12 CBD | [U-100% 13C; U-100% 15N] | 1 (±0.05) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±1.0) mM | |
4 | H2O | natural abundance | 90 (±1.0) % | |
5 | D2O | natural abundance | 10 (±1.0) % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.1) K, pH 6.0 (±0.1), Details 13C, 15N Blo t 12 CBD
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Blo t 12 CBD | [U-100% 13C; U-100% 15N] | 1 (±0.05) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±1.0) mM | |
4 | H2O | natural abundance | 90 (±1.0) % | |
5 | D2O | natural abundance | 10 (±1.0) % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.1) K, pH 6.0 (±0.1), Details 13C, 15N Blo t 12 CBD
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Blo t 12 CBD | [U-100% 13C; U-100% 15N] | 1 (±0.05) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±1.0) mM | |
4 | H2O | natural abundance | 90 (±1.0) % | |
5 | D2O | natural abundance | 10 (±1.0) % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.1) K, pH 6.0 (±0.1), Details 13C, 15N Blo t 12 CBD
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Blo t 12 CBD | [U-100% 13C; U-100% 15N] | 1 (±0.05) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±1.0) mM | |
4 | H2O | natural abundance | 90 (±1.0) % | |
5 | D2O | natural abundance | 10 (±1.0) % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.1) K, pH 6.0 (±0.1), Details 13C, 15N Blo t 12 CBD
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Blo t 12 CBD | [U-100% 13C; U-100% 15N] | 1 (±0.05) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±1.0) mM | |
4 | H2O | natural abundance | 90 (±1.0) % | |
5 | D2O | natural abundance | 10 (±1.0) % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.1) K, pH 6.0 (±0.1), Details 13C, 15N Blo t 12 CBD
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Blo t 12 CBD | [U-100% 13C; U-100% 15N] | 1 (±0.05) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±1.0) mM | |
4 | H2O | natural abundance | 90 (±1.0) % | |
5 | D2O | natural abundance | 10 (±1.0) % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.1) K, pH 6.0 (±0.1), Details 13C, 15N Blo t 12 CBD
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Blo t 12 CBD | [U-100% 13C; U-100% 15N] | 1 (±0.05) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±1.0) mM | |
4 | H2O | natural abundance | 90 (±1.0) % | |
5 | D2O | natural abundance | 10 (±1.0) % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.1) K, pH 6.0 (±0.1), Details 13C, 15N Blo t 12 CBD
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Blo t 12 CBD | [U-100% 13C; U-100% 15N] | 1 (±0.05) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | sodium chloride | natural abundance | 100 (±1.0) mM | |
4 | H2O | natural abundance | 90 (±1.0) % | |
5 | D2O | natural abundance | 10 (±1.0) % |
Bruker Avance - 600 MHz
State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 (±0.1) K, pH 6.0 (±0.1), Details 15N Blo t 12 CBD in Pf1 phage alignment medium.
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
11 | Blo t 12 CBD | [U-100% 15N] | 1 (±0.05) mM | |
12 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
13 | sodium chloride | natural abundance | 100 (±1.0) mM | |
14 | Pf1 phage | natural abundance | 11 (±0.1) mg/mL | |
15 | H2O | natural abundance | 90 (±0.1) % | |
16 | D2O | natural abundance | 10 (±0.1) % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints | combined_19553_2mfk.nef |
Input source #2: Coordindates | 2mfk.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:94:CYS:SG | A:112:CYS:SG | oxidized, CA 53.491, CB 41.492 ppm | oxidized, CA 57.242, CB 43.955 ppm | 2.027 |
A:126:CYS:SG | A:139:CYS:SG | oxidized, CA 53.556, CB 38.277 ppm | oxidized, CA 56.188, CB 40.808 ppm | 2.022 |
Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
NoneSequence alignments
----80--------90-------100-------110-------120-------130-------140--- GPLGSDLIVHEGGKTYHVVCHEEGPIPHPGNVHKYIICSKSGSLWYITVMPCSIGTKFDPISRNCVLDN ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GPLGSDLIVHEGGKTYHVVCHEEGPIPHPGNVHKYIICSKSGSLWYITVMPCSIGTKFDPISRNCVLDN --------10--------20--------30--------40--------50--------60---------
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 69 | 0 | 0 | 100.0 |
Content subtype: combined_19553_2mfk.nef
Assigned chemical shifts
----80--------90-------100-------110-------120-------130-------140--- GPLGSDLIVHEGGKTYHVVCHEEGPIPHPGNVHKYIICSKSGSLWYITVMPCSIGTKFDPISRNCVLDN |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| .PLGSDLIVHEGGKTYHVVCHEEGPIPHPGNVHKYIICSKSGSLWYITVMPCSIGTKFDPISRNCVLDN
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 402 | 392 | 97.5 |
13C chemical shifts | 310 | 292 | 94.2 |
15N chemical shifts | 68 | 66 | 97.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 140 | 136 | 97.1 |
13C chemical shifts | 138 | 128 | 92.8 |
15N chemical shifts | 63 | 61 | 96.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 262 | 256 | 97.7 |
13C chemical shifts | 172 | 164 | 95.3 |
15N chemical shifts | 5 | 5 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 38 | 38 | 100.0 |
13C chemical shifts | 38 | 38 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 33 | 27 | 81.8 |
13C chemical shifts | 32 | 24 | 75.0 |
15N chemical shifts | 1 | 1 | 100.0 |
Covalent bonds
Distance restraints
----80--------90-------100-------110-------120-------130-------140--- GPLGSDLIVHEGGKTYHVVCHEEGPIPHPGNVHKYIICSKSGSLWYITVMPCSIGTKFDPISRNCVLDN |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| .PLGSDLIVHEGGKTYHVVCHEEGPIPHPGNVHKYIICSKSGSLWYITVMPCSIGTKFDPISRNCVLDN
Dihedral angle restraints
----80--------90-------100-------110-------120-------130-------140--- GPLGSDLIVHEGGKTYHVVCHEEGPIPHPGNVHKYIICSKSGSLWYITVMPCSIGTKFDPISRNCVLDN |||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||| ...GSDLIVHEGGKTYHVVCH...PIPHPGNVHKYIICSKSGSLWYITVMPCSIGTKFDPISRNCVLDN
RDC restraints
----80--------90-------100-------110-------120-------130-------140--- GPLGSDLIVHEGGKTYHVVCHEEGPIPHPGNVHKYIICSKSGSLWYITVMPCSIGTKFDPISRNCVLDN |||||||| |||||||| ||| | | ||| ||||||||||||||||| || ||||| ||||| ||| ...GSDLIVHE.GKTYHVVC.EEG.I.H.GNV.KYIICSKSGSLWYITVM.CS.GTKFD.ISRNC.LDN