BMRB Entry 36086
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR36086
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Title: Solution structure of the major fish allergen parvalbumin Sco j 1 derived from the Pacific mackerel PubMed: 29215073
Deposition date: 2017-05-22 Original release date: 2017-12-26
Authors: Kumeta, H.; Nakayama, H.; Ogura, K.
Citation: Kumeta, H.; Nakayama, H.; Ogura, K.. "Solution structure of the major fish allergen parvalbumin Sco j 1 derived from the Pacific mackerel" Sci. Rep. 7, 17160-17160 (2017).
Assembly members:
Parvalbumin beta, polymer, 114 residues, 11973.583 Da.
CALCIUM ION, non-polymer, 40.078 Da.
Natural source: Common Name: Chub mackerel Taxonomy ID: 13676 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Scomber japonicus
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
Parvalbumin beta: GPLGSMAFASVLKDAEVTAA
LDGCKAAGSFDHKKFFKACG
LSGKSTDEVKKAFAIIDQDK
SGFIEEEELKLFLQNFKAGA
RALSDAETKAFLKAGDSDGD
GKIGIDEFAAMIKG
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 458 |
| 15N chemical shifts | 113 |
| 1H chemical shifts | 746 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_CA_1 | 2 |
| 3 | entity_CA_2 | 2 |
Entities:
Entity 1, entity_1 114 residues - 11973.583 Da.
| 1 | GLY | PRO | LEU | GLY | SER | MET | ALA | PHE | ALA | SER | ||||
| 2 | VAL | LEU | LYS | ASP | ALA | GLU | VAL | THR | ALA | ALA | ||||
| 3 | LEU | ASP | GLY | CYS | LYS | ALA | ALA | GLY | SER | PHE | ||||
| 4 | ASP | HIS | LYS | LYS | PHE | PHE | LYS | ALA | CYS | GLY | ||||
| 5 | LEU | SER | GLY | LYS | SER | THR | ASP | GLU | VAL | LYS | ||||
| 6 | LYS | ALA | PHE | ALA | ILE | ILE | ASP | GLN | ASP | LYS | ||||
| 7 | SER | GLY | PHE | ILE | GLU | GLU | GLU | GLU | LEU | LYS | ||||
| 8 | LEU | PHE | LEU | GLN | ASN | PHE | LYS | ALA | GLY | ALA | ||||
| 9 | ARG | ALA | LEU | SER | ASP | ALA | GLU | THR | LYS | ALA | ||||
| 10 | PHE | LEU | LYS | ALA | GLY | ASP | SER | ASP | GLY | ASP | ||||
| 11 | GLY | LYS | ILE | GLY | ILE | ASP | GLU | PHE | ALA | ALA | ||||
| 12 | MET | ILE | LYS | GLY |
Entity 2, entity_CA_1 - Ca - 40.078 Da.
| 1 | CA |
Samples:
sample_1: Sco j 1, [U-13C; U-15N], 0.5 mM; CaCl2 10 mM; sodium chloride 150 mM; MES 20 mM; H2O 93%; D2O, [U-2H], 7%
sample_conditions_1: ionic strength: 180 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CA)HA | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 3D HCCH-TOCSY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D HbCbCgCdHd | sample_1 | isotropic | sample_conditions_1 |
| 2D HbCbCgCdCeHe | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY aromatic | sample_1 | isotropic | sample_conditions_1 |
Software:
CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure calculation
NMRPipe v8.2, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
SPARKY v3.113, Goddard - chemical shift assignment
TALOS+ v3.80F1, Shen, Delaglio, Cornilescu, Bax - data analysis
TOPSPIN v3.2, Bruker Biospin - collection
VNMR v6.1C, Varian - collection
NMR spectrometers:
- Bruker AvanceIII HD 800 MHz
- Varian UNITY 600 MHz
- Varian UNITY 500 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts