BMRB Entry 26336
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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/BMR26336
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Title: Solution Structure of the Corynebacterium diphtheriae SpaB
Deposition date: 2023-05-04 Original release date: 2023-06-18
Authors: Sue, Christopher; Cheung, Nicole; Mahoney, Brendan; Clubb, Robert
Citation: Sue, Christopher; Cheung, Nicole; Mahoney, Brendan; McConnell, Scott; Scully, Jack; Fu, Janine; Chang, Chungyu; Ton-That, Hung; Loo, Joseph; Clubb, Robert. "The basal and major pilins in the Corynebacterium diphtheriae SpaA pilus adopt similar structures that competitively react with the pilin polymerase" Biopolymers ., .-..
Assembly members:
SpaB, polymer, 126 residues, Formula weight is not available
Natural source: Common Name: Corynebacterium diphtheriae NCTC 13129 Taxonomy ID: 257309 Superkingdom: Bacteria Kingdom: not available Genus/species: Corynebacterium diphtheriae
Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3) Vector: pSUMO
Entity Sequences (FASTA):
SpaB: QEANTLVIDLEPPAAFADDQ
PQGHNIDVTVAKLHNIDPED
HERIRALQRNGVPSTISEEQ
PHTARTDATGTATITNLPPG
TYVIRDTNTTKPRFSPLVIP
LGIDTTSPTMTLRPKLIDAT
PGAPNV
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 501 |
| 15N chemical shifts | 119 |
| 1H chemical shifts | 749 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | SpaB | 1 |
Entities:
Entity 1, SpaB 126 residues - Formula weight is not available
Soluble domain of SpaB
| 1 | GLN | GLU | ALA | ASN | THR | LEU | VAL | ILE | ASP | LEU | ||||
| 2 | GLU | PRO | PRO | ALA | ALA | PHE | ALA | ASP | ASP | GLN | ||||
| 3 | PRO | GLN | GLY | HIS | ASN | ILE | ASP | VAL | THR | VAL | ||||
| 4 | ALA | LYS | LEU | HIS | ASN | ILE | ASP | PRO | GLU | ASP | ||||
| 5 | HIS | GLU | ARG | ILE | ARG | ALA | LEU | GLN | ARG | ASN | ||||
| 6 | GLY | VAL | PRO | SER | THR | ILE | SER | GLU | GLU | GLN | ||||
| 7 | PRO | HIS | THR | ALA | ARG | THR | ASP | ALA | THR | GLY | ||||
| 8 | THR | ALA | THR | ILE | THR | ASN | LEU | PRO | PRO | GLY | ||||
| 9 | THR | TYR | VAL | ILE | ARG | ASP | THR | ASN | THR | THR | ||||
| 10 | LYS | PRO | ARG | PHE | SER | PRO | LEU | VAL | ILE | PRO | ||||
| 11 | LEU | GLY | ILE | ASP | THR | THR | SER | PRO | THR | MET | ||||
| 12 | THR | LEU | ARG | PRO | LYS | LEU | ILE | ASP | ALA | THR | ||||
| 13 | PRO | GLY | ALA | PRO | ASN | VAL |
Samples:
sample_1: SpaB, [U-100% 13C; U-100% 15N], 1.2 mM; sodium azide 0.01%; sodium chloride 100 mM; sodium phosphate 50 mM; H2O 93%; D2O, [U-2H], 7%
sample_2: SpaB, [U-100% 13C; U-100% 15N], 1.2 mM; sodium azide 0.01%; sodium chloride 100 mM; sodium phosphate 50 mM; D2O, [U-2H], 100%
sample_conditions_1: ionic strength: 100 mM; pH: 6.5; 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_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | 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 HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNHA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNHB | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | sample_2 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
Software:
X-PLOR NIH v2.37 - structure solution
TOPSPIN v3.5 - collection
NMRPipe v11.1 - data analysis
Xipp v1.21.7 - peak picking, refinement
NMRFAM-SPARKY - data analysis
CARA v1.9.1.7 - chemical shift assignment
Molmol - refinement
ProcheckNMR - geometry optimization
NMR spectrometers:
- Bruker AVANCE III 600 MHz
- Bruker AVANCE NEO 800 MHz
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts