BMRB Entry 30611
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30611
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Title: NMR solution structure of YfiD PubMed: 31250200
Deposition date: 2019-05-10 Original release date: 2019-07-05
Authors: Bowman, S.; Drennan, C.
Citation: Bowman, S.; Backman, L.; Bjork, R.; Andorfer, M.; Yori, S.; Caruso, A.; Stultz, C.; Drennan, C.. "Solution structure and biochemical characterization of a spare part protein that restores activity to an oxygen-damaged glycyl radical enzyme." J. Biol. Inorg. Chem. ., .-. (2019).
Assembly members:
entity_1, polymer, 127 residues, 14286.153 Da.
Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity_1: MITGIQITKAANDDLLNSFW
LLDSEKGEARCIVAKAGFAE
DEVVAVSKLGDIEYREVPVE
VKPEVRVEGGQHLNVNVLRR
ETLEDAVKHPEKYPQLTIRV
SGYAVRFNSLTPEQQRDVIA
RTFTESL
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 76 |
| 15N chemical shifts | 57 |
| 1H chemical shifts | 349 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
Entities:
Entity 1, entity_1 127 residues - 14286.153 Da.
| 1 | MET | ILE | THR | GLY | ILE | GLN | ILE | THR | LYS | ALA | ||||
| 2 | ALA | ASN | ASP | ASP | LEU | LEU | ASN | SER | PHE | TRP | ||||
| 3 | LEU | LEU | ASP | SER | GLU | LYS | GLY | GLU | ALA | ARG | ||||
| 4 | CYS | ILE | VAL | ALA | LYS | ALA | GLY | PHE | ALA | GLU | ||||
| 5 | ASP | GLU | VAL | VAL | ALA | VAL | SER | LYS | LEU | GLY | ||||
| 6 | ASP | ILE | GLU | TYR | ARG | GLU | VAL | PRO | VAL | GLU | ||||
| 7 | VAL | LYS | PRO | GLU | VAL | ARG | VAL | GLU | GLY | GLY | ||||
| 8 | GLN | HIS | LEU | ASN | VAL | ASN | VAL | LEU | ARG | ARG | ||||
| 9 | GLU | THR | LEU | GLU | ASP | ALA | VAL | LYS | HIS | PRO | ||||
| 10 | GLU | LYS | TYR | PRO | GLN | LEU | THR | ILE | ARG | VAL | ||||
| 11 | SER | GLY | TYR | ALA | VAL | ARG | PHE | ASN | SER | LEU | ||||
| 12 | THR | PRO | GLU | GLN | GLN | ARG | ASP | VAL | ILE | ALA | ||||
| 13 | ARG | THR | PHE | THR | GLU | SER | LEU |
Samples:
sample_1: YfiD, [U-15N], 0.7 mM; HEPES 18 mM; ammonium sulfate 2.7 mM; D2O 10 % v/v
sample_2: YfiD, [U-100% 13C; U-100% 15N], 1.3 mM; HEPES 18 mM; ammonium sulfate 2.7 mM; D2O 10 % v/v
sample_conditions_1: ionic strength: 2.7 mM; pH: 7.2; pressure: 760 mmHg; temperature: 293 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_2 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_2 | isotropic | sample_conditions_1 |
Software:
VNMR, Varian - collection
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
Sparky, Goddard - chemical shift assignment, peak picking, structure calculation
CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation
NMR spectrometers:
- Varian INOVA 800 MHz
- FBML CMR 600 E 600 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts