BMRB Entry 30800
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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/BMR30800
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Title: Solution Structure of the Corynebacterium diphtheriae SpaA Pilin-Signal Peptide Complex PubMed: 33723052
Deposition date: 2020-09-22 Original release date: 2021-03-04
Authors: McConnell, S.; Clubb, R.
Citation: McConnell, S.; McAllister, R.; Amer, B.; Mahoney, B.; Sue, C.; Chang, C.; Ton-That, H.; Clubb, R.. "Sortase-assembled pili in Corynebacterium diphtheriae are built using a latch mechanism" Proc. Natl. Acad. Sci. U. S. A. 118, .-. (2021).
Assembly members:
entity_1, polymer, 143 residues, 15399.396 Da.
entity_2, polymer, 10 residues, 1090.249 Da.
Natural source: Common Name: Corynebacterium diphtheriae 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):
entity_1: ERTSIAVHALMGLPTGQPAN
GTKLDSIGLPKVDGMSFTLY
RVNEIDLTTQAGWDAASKIK
LEELYTNGHPTDKVTKVATK
KTEGGVAKFDNLTPALYLVV
QELNGAEAVVRSQPFLVAAP
QTNPTGDGWLQDVHVYPKHQ
ALS
entity_2: KNAGFELPLT
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 600 |
| 15N chemical shifts | 137 |
| 1H chemical shifts | 954 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | unit_1 | 1 |
| 2 | unit_2 | 2 |
Entities:
Entity 1, unit_1 143 residues - 15399.396 Da.
| 1 | GLU | ARG | THR | SER | ILE | ALA | VAL | HIS | ALA | LEU | ||||
| 2 | MET | GLY | LEU | PRO | THR | GLY | GLN | PRO | ALA | ASN | ||||
| 3 | GLY | THR | LYS | LEU | ASP | SER | ILE | GLY | LEU | PRO | ||||
| 4 | LYS | VAL | ASP | GLY | MET | SER | PHE | THR | LEU | TYR | ||||
| 5 | ARG | VAL | ASN | GLU | ILE | ASP | LEU | THR | THR | GLN | ||||
| 6 | ALA | GLY | TRP | ASP | ALA | ALA | SER | LYS | ILE | LYS | ||||
| 7 | LEU | GLU | GLU | LEU | TYR | THR | ASN | GLY | HIS | PRO | ||||
| 8 | THR | ASP | LYS | VAL | THR | LYS | VAL | ALA | THR | LYS | ||||
| 9 | LYS | THR | GLU | GLY | GLY | VAL | ALA | LYS | PHE | ASP | ||||
| 10 | ASN | LEU | THR | PRO | ALA | LEU | TYR | LEU | VAL | VAL | ||||
| 11 | GLN | GLU | LEU | ASN | GLY | ALA | GLU | ALA | VAL | VAL | ||||
| 12 | ARG | SER | GLN | PRO | PHE | LEU | VAL | ALA | ALA | PRO | ||||
| 13 | GLN | THR | ASN | PRO | THR | GLY | ASP | GLY | TRP | LEU | ||||
| 14 | GLN | ASP | VAL | HIS | VAL | TYR | PRO | LYS | HIS | GLN | ||||
| 15 | ALA | LEU | SER |
Entity 2, unit_2 10 residues - 1090.249 Da.
| 1 | LYS | ASN | ALA | GLY | PHE | GLU | LEU | PRO | LEU | THR |
Samples:
sample_1: SpaA backbone pilin for protein, [U-13C; U-15N], 1.2 mM; SpaA sorting signal for peptide 1.2 mM; NaH2PO4 50 mM; NaCl 100 mM; NaN3 0.01%
sample_2: SpaA backbone pilin for protein, [U-13C; U-15N], 1.2 mM; SpaA sorting signal for peptide 1.2 mM; NaH2PO4 50 mM; NaCl 100 mM; NaN3 0.01%
sample_conditions_1: ionic strength: 100 mM; pH: 6.0; pressure: 1 .; temperature: 298 K
sample_conditions_2: ionic strength: 100 mM; pH: 6.0; pressure: 1 .; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D_15N-separated_NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D_(F1)_13C,15N-filtered_(F2)_15N-edited NOESY-HSQC | sample_1 | isotropic | sample_conditions_2 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_2 | isotropic | sample_conditions_2 |
| 2D 1H-13C HSQC aromatic | sample_2 | isotropic | sample_conditions_2 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 1H-15N heteronoe | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| T2/R2 relaxation | sample_1 | isotropic | sample_conditions_1 |
| T1/R1 relaxation | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | sample_2 | isotropic | sample_conditions_2 |
| 3D HNHA | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 2D (F1,F2) 13C-filtered NOESY | sample_2 | isotropic | sample_conditions_2 |
| 2D (F1) 13C,15N-filtered TOCSY | sample_2 | isotropic | sample_conditions_2 |
| 3D_(F1)_13C,15N-filtered_(F2)_13C-edited NOESY-HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D_13C-separated_NOESY_aliphatic_D2O | sample_2 | isotropic | sample_conditions_2 |
| 3D_13C-separated_NOESY_aromatic_D2O | sample_2 | isotropic | sample_conditions_1 |
| 3D_13C-separated_NOESY_aliphatic_H2O | sample_1 | isotropic | sample_conditions_1 |
Software:
X-PLOR NIH v2.37, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation
Xipp v1.19, Dan Garrett - chemical shift assignment, peak picking
UNIO, Torsten Herrmann - structure calculation
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
TopSpin, Bruker Biospin - collection
NMRFAM-SPARKY, National Magnetic Resonance Facility at Madison (Wisconsin) - data analysis
CARA, Keller and Wuthrich - peak picking
TALOS-N, Cornilescu, Delaglio and Bax - geometry optimization
MOLMOL, Koradi, Billeter and Wuthrich - refinement
PROCHECK / PROCHECK-NMR, Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thornton - refinement
NMR spectrometers:
- Bruker AVANCE III HD 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