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
MolProbity Validation Chart

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Title:
Solution structure of the major fish allergen parvalbumin Sco j 1 derived from the Pacific mackerel
Deposition date:
2017-05-22
Original release date:
2017-12-26
Authors:
Kumeta, H.; Nakayama, H.; Ogura, K.
Citation:

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).
PubMed: 29215073

Assembly members:

Assembly members:
Parvalbumin beta, polymer, 114 residues, 11973.583 Da.
CALCIUM ION, non-polymer, 40.078 Da.

Natural source:

Natural source:   Common Name: Chub mackerel   Taxonomy ID: 13676   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Scomber japonicus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Parvalbumin beta: GPLGSMAFASVLKDAEVTAA LDGCKAAGSFDHKKFFKACG LSGKSTDEVKKAFAIIDQDK SGFIEEEELKLFLQNFKAGA RALSDAETKAFLKAGDSDGD GKIGIDEFAAMIKG

Data sets:
Data typeCount
13C chemical shifts458
15N chemical shifts113
1H chemical shifts746

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_CA_12
3entity_CA_22

Entities:

Entity 1, entity_1 114 residues - 11973.583 Da.

1   GLYPROLEUGLYSERMETALAPHEALASER
2   VALLEULYSASPALAGLUVALTHRALAALA
3   LEUASPGLYCYSLYSALAALAGLYSERPHE
4   ASPHISLYSLYSPHEPHELYSALACYSGLY
5   LEUSERGLYLYSSERTHRASPGLUVALLYS
6   LYSALAPHEALAILEILEASPGLNASPLYS
7   SERGLYPHEILEGLUGLUGLUGLULEULYS
8   LEUPHELEUGLNASNPHELYSALAGLYALA
9   ARGALALEUSERASPALAGLUTHRLYSALA
10   PHELEULYSALAGLYASPSERASPGLYASP
11   GLYLYSILEGLYILEASPGLUPHEALAALA
12   METILELYSGLY

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HN(CA)HAsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 3D HCCH-TOCSY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
2D HbCbCgCdHdsample_1isotropicsample_conditions_1
2D HbCbCgCdCeHesample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D HCCH-TOCSY aromaticsample_1isotropicsample_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 HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks