BMRB Entry 15477
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15477
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Title: Solution structure of the extracellular domain of Prod1, a protein implicated in proximodistal identity during amphibian limb regeneration PubMed: 19771161
Deposition date: 2007-09-19 Original release date: 2009-10-14
Authors: Garza-Garcia, Acely; Harris, Richard; Esposito, Diego; Driscoll, Paul
Citation: Garza-Garcia, Acely; Harris, Richard; Esposito, Diego; Gates, Phillip; Driscoll, Paul. "Solution structure and phylogenetics of Prod1, a member of the three-finger protein superfamily implicated in salamander limb regeneration." PLoS One 4, 7123-. (2009).
Assembly members:
Prod1, polymer, 91 residues, 10208.4 Da.
Natural source: Common Name: Eastern newt Taxonomy ID: 8316 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Notophthalmus viridescens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
Prod1: MGSSHHHHHHSSGLVPRGSH
MALKCFTRNGDDRTVTTCAE
EQTRCLFVQLPYSEIQECKT
VQQCAEVLEEVTAIGYPAKC
CCEDLCNRSEQ
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 300 |
| 15N chemical shifts | 69 |
| 1H chemical shifts | 461 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Prod1 | 1 |
Entities:
Entity 1, Prod1 91 residues - 10208.4 Da.
His Tag MGSSHHHHHH SSGLVPRGSH M Protein Sequence ALKCFTRNGDDRTVTTCAEEQTRCLFVQLPYSEIQECKTVQQCAEVLEEVTAIGYPAKCCCEDLCNRSEQ
| 1 | MET | GLY | SER | SER | HIS | HIS | HIS | HIS | HIS | HIS | ||||
| 2 | SER | SER | GLY | LEU | VAL | PRO | ARG | GLY | SER | HIS | ||||
| 3 | MET | ALA | LEU | LYS | CYS | PHE | THR | ARG | ASN | GLY | ||||
| 4 | ASP | ASP | ARG | THR | VAL | THR | THR | CYS | ALA | GLU | ||||
| 5 | GLU | GLN | THR | ARG | CYS | LEU | PHE | VAL | GLN | LEU | ||||
| 6 | PRO | TYR | SER | GLU | ILE | GLN | GLU | CYS | LYS | THR | ||||
| 7 | VAL | GLN | GLN | CYS | ALA | GLU | VAL | LEU | GLU | GLU | ||||
| 8 | VAL | THR | ALA | ILE | GLY | TYR | PRO | ALA | LYS | CYS | ||||
| 9 | CYS | CYS | GLU | ASP | LEU | CYS | ASN | ARG | SER | GLU | ||||
| 10 | GLN |
Samples:
sample_1: Prod1, [U-15N], 1 mM; sodium phosphate 50 mM; sodium chloride 150 mM; EDTA 1 mM; H2O 90%; D2O 10%
sample_2: Prod1, [U-13C; U-15N], 1 mM; sodium phosphate 50 mM; sodium chloride 150 mM; EDTA 1 mM; H2O 90%; D2O 10%
sample_3: Prod1, [U-13C; U-15N], 1 mM; sodium phosphate 50 mM; sodium chloride 150 mM; EDTA 1 mM; D2O 100%
sample_conditions_1: ionic strength: 0.2 M; 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 | sample_3 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_3 | isotropic | sample_conditions_1 |
| 3D 1H-13C aromatic NOESY | sample_3 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_2 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_2 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | sample_2 | isotropic | sample_conditions_1 |
| 3D HA(CA)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HN(CACO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_3 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | sample_3 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_1 | isotropic | sample_conditions_1 |
Software:
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
ANSIG, Kraulis - data analysis
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution
NMR spectrometers:
- Varian INOVA 800 MHz
- Varian INOVA 600 MHz
- Varian INOVA 600 MHz
- Varian UnityPlus 500 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts