BMRB Entry 34424
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR34424
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Title: Precursor structure of the self-processing module of iron-regulated FrpC of N. Meningitidis with calcium ions PubMed: 32184239
Deposition date: 2019-08-14 Original release date: 2020-02-20
Authors: Kuban, V.; Macek, P.; Hritz, J.; Nechvatalova, K.; Nedbalcova, K.; Faldyna, M.; Zidek, L.; Bumba, L.
Citation: Kuban, V.; Macek, P.; Hritz, J.; Nechvatalova, K.; Nedbalcova, K.; Faldyna, M.; Zidek, L.; Bumba, L.. "Structural basis of Ca 2+ -dependent self-processing activity of repeat-in-toxin proteins" mBio 11, e00226-20-e00226-20 (2020).
Assembly members:
entity_1, polymer, 182 residues, 19246.879 Da.
entity_CA, non-polymer, 40.078 Da.
Natural source: Common Name: Neisseria meningitidis Taxonomy ID: 135720 Superkingdom: Bacteria Kingdom: not available Genus/species: Neisseria meningitidis
Experimental source: Production method: recombinant technology Host organism: Escherichia coli K-12
Entity Sequences (FASTA):
entity_1: GSDALALDLDGDGIETVATK
GFSGSLFDHNRDGIRTATGW
VSADDGLLVRDLNGNGIIDN
GAELFGDNTKLADGSFAKHG
YAALAELDSNGDNIINAADA
AFQSLRVWQDLNQDGISQAN
ELRTLEELGIQSLDLAYKDV
NKNLGNGNTLAQQGSYTKTN
GTTAKMGDLLLAADNLHSRF
LE
| Data type | Count |
| 13C chemical shifts | 576 |
| 15N chemical shifts | 156 |
| 1H chemical shifts | 933 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_2, 1 | 2 |
| 3 | entity_2, 2 | 2 |
| 4 | entity_2, 3 | 2 |
| 5 | entity_2, 4 | 2 |
| 6 | entity_2, 5 | 2 |
Entities:
Entity 1, entity_1 182 residues - 19246.879 Da.
| 1 | GLY | SER | ASP | ALA | LEU | ALA | LEU | ASP | LEU | ASP | ||||
| 2 | GLY | ASP | GLY | ILE | GLU | THR | VAL | ALA | THR | LYS | ||||
| 3 | GLY | PHE | SER | GLY | SER | LEU | PHE | ASP | HIS | ASN | ||||
| 4 | ARG | ASP | GLY | ILE | ARG | THR | ALA | THR | GLY | TRP | ||||
| 5 | VAL | SER | ALA | ASP | ASP | GLY | LEU | LEU | VAL | ARG | ||||
| 6 | ASP | LEU | ASN | GLY | ASN | GLY | ILE | ILE | ASP | ASN | ||||
| 7 | GLY | ALA | GLU | LEU | PHE | GLY | ASP | ASN | THR | LYS | ||||
| 8 | LEU | ALA | ASP | GLY | SER | PHE | ALA | LYS | HIS | GLY | ||||
| 9 | TYR | ALA | ALA | LEU | ALA | GLU | LEU | ASP | SER | ASN | ||||
| 10 | GLY | ASP | ASN | ILE | ILE | ASN | ALA | ALA | ASP | ALA | ||||
| 11 | ALA | PHE | GLN | SER | LEU | ARG | VAL | TRP | GLN | ASP | ||||
| 12 | LEU | ASN | GLN | ASP | GLY | ILE | SER | GLN | ALA | ASN | ||||
| 13 | GLU | LEU | ARG | THR | LEU | GLU | GLU | LEU | GLY | ILE | ||||
| 14 | GLN | SER | LEU | ASP | LEU | ALA | TYR | LYS | ASP | VAL | ||||
| 15 | ASN | LYS | ASN | LEU | GLY | ASN | GLY | ASN | THR | LEU | ||||
| 16 | ALA | GLN | GLN | GLY | SER | TYR | THR | LYS | THR | ASN | ||||
| 17 | GLY | THR | THR | ALA | LYS | MET | GLY | ASP | LEU | LEU | ||||
| 18 | LEU | ALA | ALA | ASP | ASN | LEU | HIS | SER | ARG | PHE | ||||
| 19 | LEU | GLU |
Entity 2, entity_2, 1 - Ca - 40.078 Da.
| 1 | CA |
Samples:
sample_1: TRIS 5 mM; sodium chloride 50 mM; sodium azide 0.1%; Calcium chloride 10 mM; P415A mutant of Self-processing module of FrpC, [U-99% 13C; U-99% 15N], 0.35 ± 0.05 mM
sample_2: TRIS 50 mM; sodium chloride 50 mM; sodium azide 0.1%; P415A mutant of Self-processing module of FrpC 0.707 ± 0.005 mM
sample_conditions_1: ionic strength: 65 mM; pH: 7.4; pressure: 1 atm; temperature: 303.2 K
sample_conditions_2: ionic strength: 100 mM; pH: 7.4; pressure: 1 atm; temperature: 303.2 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 1D WATERGATE W5 | sample_2 | isotropic | sample_conditions_2 |
Software:
Sparky v3.115, Goddard - chemical shift assignment, data analysis, peak picking
TopSpin v3.2, Bruker Biospin - collection, processing
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
CYANA v3.97, Guntert, Mumenthaler and Wuthrich - structure calculation
GROMACS v5.1.1, Erik Lindahl, David van der Spoel, Berk Hess, Mark Abraham - refinement
NMR spectrometers:
- Bruker AVANCE III 600.05 MHz
- Bruker AVANCE III 950.33 MHz
- Bruker AVANCE III 850.28 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts