BMRB Entry 30686
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30686
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Title: Solution structure of AGL55-Kringle 2 complex
Deposition date: 2019-11-14 Original release date: 2020-12-04
Authors: Qiu, C.; Yuan, Y.; Castellino, F.
Citation: Qiu, C.; Yuan, Y.; Ploplis, V.; Castellino, F.. "Structural evolution of the A-domain in plasminogen-binding Group A streptococcal M-protein reflects improved adaptability of the pathogen to the host" .
Assembly members:
entity_1, polymer, 87 residues, 10166.340 Da.
entity_2, polymer, 57 residues, 6742.396 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Komagataella pastoris
Entity Sequences (FASTA):
entity_1: YVEFSEECMHGSGENYDGKI
SKTMSGLECQAWDSQSPHAH
GYIPSKFPNKNLKKNYCRNP
DRDLRPWCFTTDPNKRWEYC
DIPRCAA
entity_2: GSAGLQEKERELEDLKDAEL
KRLNEERHDHDKREAERKAL
EDKLADKQEHLDGALRY
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 220 |
| 15N chemical shifts | 52 |
| 1H chemical shifts | 333 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_2 | 2 |
Entities:
Entity 1, entity_1 87 residues - 10166.340 Da.
| 1 | TYR | VAL | GLU | PHE | SER | GLU | GLU | CYS | MET | HIS | ||||
| 2 | GLY | SER | GLY | GLU | ASN | TYR | ASP | GLY | LYS | ILE | ||||
| 3 | SER | LYS | THR | MET | SER | GLY | LEU | GLU | CYS | GLN | ||||
| 4 | ALA | TRP | ASP | SER | GLN | SER | PRO | HIS | ALA | HIS | ||||
| 5 | GLY | TYR | ILE | PRO | SER | LYS | PHE | PRO | ASN | LYS | ||||
| 6 | ASN | LEU | LYS | LYS | ASN | TYR | CYS | ARG | ASN | PRO | ||||
| 7 | ASP | ARG | ASP | LEU | ARG | PRO | TRP | CYS | PHE | THR | ||||
| 8 | THR | ASP | PRO | ASN | LYS | ARG | TRP | GLU | TYR | CYS | ||||
| 9 | ASP | ILE | PRO | ARG | CYS | ALA | ALA |
Entity 2, entity_2 57 residues - 6742.396 Da.
| 1 | GLY | SER | ALA | GLY | LEU | GLN | GLU | LYS | GLU | ARG | ||||
| 2 | GLU | LEU | GLU | ASP | LEU | LYS | ASP | ALA | GLU | LEU | ||||
| 3 | LYS | ARG | LEU | ASN | GLU | GLU | ARG | HIS | ASP | HIS | ||||
| 4 | ASP | LYS | ARG | GLU | ALA | GLU | ARG | LYS | ALA | LEU | ||||
| 5 | GLU | ASP | LYS | LEU | ALA | ASP | LYS | GLN | GLU | HIS | ||||
| 6 | LEU | ASP | GLY | ALA | LEU | ARG | TYR |
Samples:
sample_1: AGL55, [U-99% 13C; U-99% 15N], 1.0 ± 0.1 mM; Kringle 2 1.2 ± 0.1 mM; Bis-Tris-d19, [U-2H], 20 mM; DSS 2 ug/mL; sodium azide 2 ug/mL
sample_2: AGL55 1.2 ± 0.1 mM; Kringle 2, [U-99% 13C; U-99% 15N], 1.0 ± 0.1 mM; Bis-Tris-d19, [U-2H], 20 mM; DSS 2 ug/mL; sodium azide 2 ug/mL
sample_conditions_1: ionic strength: 20 mM; pH: 6.7; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D TROSY-[1H-15N] HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D TROSY-HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D TROSY-HN(CA)CO | sample_1 | isotropic | sample_conditions_1 |
| 3D TROSY-HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D TROSY-C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D TROSY-HBHA(CBCA)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D TROSY-H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 2D NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D IPAP | sample_1 | anisotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D IPAP | sample_2 | anisotropic | sample_conditions_1 |
Software:
TopSpin, Bruker Biospin - collection, processing
Sparky, Goddard - data analysis
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation
HADDOCK, Bonvin - refinement
NMR spectrometers:
- Bruker AVANCE 800 MHz
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts