BMRB Entry 19227
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR19227
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Title: Human Pdx1 Homeodomain in the Unbound State PubMed: 23796517
Deposition date: 2013-05-06 Original release date: 2013-07-29
Authors: Showalter, Scott; Bastidas, Monique
Citation: Bastidas, Monique; Showalter, Scott. "Thermodynamic and Structural Determinants of Differential Pdx1 Binding to Elements from the Insulin and IAPP Promoters." J. Mol. Biol. 425, 3360-3377 (2013).
Assembly members:
Pdx1, polymer, 64 residues, Formula weight is not available
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
Pdx1: GPGNKRTRTAYTRAQLLELE
KEFLFNKYISRPRRVELAVM
LNLTERHIKIWFQNRRMKWK
KEED
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 161 |
| 15N chemical shifts | 50 |
| 1H chemical shifts | 50 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Pdx1 | 1 |
Entities:
Entity 1, Pdx1 64 residues - Formula weight is not available
| 1 | GLY | PRO | GLY | ASN | LYS | ARG | THR | ARG | THR | ALA | ||||
| 2 | TYR | THR | ARG | ALA | GLN | LEU | LEU | GLU | LEU | GLU | ||||
| 3 | LYS | GLU | PHE | LEU | PHE | ASN | LYS | TYR | ILE | SER | ||||
| 4 | ARG | PRO | ARG | ARG | VAL | GLU | LEU | ALA | VAL | MET | ||||
| 5 | LEU | ASN | LEU | THR | GLU | ARG | HIS | ILE | LYS | ILE | ||||
| 6 | TRP | PHE | GLN | ASN | ARG | ARG | MET | LYS | TRP | LYS | ||||
| 7 | LYS | GLU | GLU | ASP |
Samples:
sample_1: Pdx1, [U-99% 13C; U-99% 15N], 300 uM; potassium cacodylate 100 mM; potassium chloride 100 mM; D2O 10%; H2O 90%
sample_2: Pdx1, [U-99% 13C; U-99% 15N], 300 uM; DNA 500 uM; potassium cacodylate 100 mM; potassium chloride 100 mM; D2O 10%; H2O 90%
sample_conditions_1: ionic strength: 0.2 M; pH: 7.3; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | 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 HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_2 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | sample_2 | isotropic | sample_conditions_1 |
Software:
SPARKY v3, Goddard - data analysis
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
TOPSPIN, Bruker Biospin - collection
NMR spectrometers:
- Bruker Avance 850 MHz
Related Database Links:
| BMRB | 19228 |
| PDB | |
| DBJ | BAB32045 BAG74161 |
| EMBL | CAA34746 CAA52389 CAA68169 |
| GB | AAA18355 AAA74012 AAA88820 AAB18252 AAB29317 |
| PIR | I65249 |
| REF | NP_000200 NP_001074947 NP_001135456 NP_001165682 NP_001179065 |
| SP | A1YF08 A1YG85 A2T756 P14837 P52945 |
| TPG | DAA23869 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts