BMRB Entry 25066
Click here to enlarge.
PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25066
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
NMR-STAR v2.1 text file (deprecated)
XML gzip file.
RDF gzip file.
All files associated with the entry
Title: NMR structure of UBA domain of DNA-damage-inducible 1 protein (Ddi1)
Deposition date: 2014-07-02 Original release date: 2015-02-02
Authors: Zhang, Daoning; Fushman, David
Citation: Nowicka, Urszula; Zhang, Daoning; Walker, Olivier; Castaneda, Calos; Krutauz, Daria; Chen, Tony; Reis, Noa; Glickman, Michael; Fushman, David. "DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain" Structure ., .-..
Assembly members:
entity, polymer, 44 residues, 4745.415 Da.
Natural source: Common Name: Baker Taxonomy ID: 4932 Superkingdom: not available Kingdom: not available Genus/species: Eukaryota Fungi
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity: GSATFPEQTIKQLMDLGFPR
DAVVKALKQTNGNAEFAASL
LFQS
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 296 |
| 15N chemical shifts | 45 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | UBA domain of DNA-damage-inducible 1 protein (Ddi1) | 1 |
Entities:
Entity 1, UBA domain of DNA-damage-inducible 1 protein (Ddi1) 44 residues - 4745.415 Da.
First three residues 'GSA' represent a non-native affinity tag. Residue 4T represents 389T in the Ddi1 sequence.
| 1 | GLY | SER | ALA | THR | PHE | PRO | GLU | GLN | THR | ILE | ||||
| 2 | LYS | GLN | LEU | MET | ASP | LEU | GLY | PHE | PRO | ARG | ||||
| 3 | ASP | ALA | VAL | VAL | LYS | ALA | LEU | LYS | GLN | THR | ||||
| 4 | ASN | GLY | ASN | ALA | GLU | PHE | ALA | ALA | SER | LEU | ||||
| 5 | LEU | PHE | GLN | SER |
Samples:
sample_1: UBA, [U-100% 15N], 1 mM; D2O, [U-99% 2H], 7%; H2O 93%; sodium phosphate 20 mM
sample_2: UBA, [U-100% 15N], 0.5 mM; D2O, [U-99% 2H], 7%; H2O 43%; sodium phosphate 10 mM; C12E5 5%; n-hexanol 45%
sample_conditions_1: temperature: 298.2 K; pH: 6.8; pressure: 1 atm; ionic strength: 10 mM
sample_conditions_2: temperature: 308.2 K; pH: 6.8; pressure: 1 atm; ionic strength: 10 mM
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_1 | isotropic | sample_conditions_1 |
| RDC | sample_2 | isotropic | sample_conditions_1 |
| RDC | sample_2 | isotropic | sample_conditions_2 |
Software:
CARA v1.8.1, Keller and Wuthrich - peak picking, chemical shift assignment
TOPSPIN v2.1, Bruker Biospin - collection, processing, data analysis
ARIA v2.1, Linge, O, . - chemical shift calculation, structure solution, refinement
NMR spectrometers:
- Bruker Avance 600 MHz
Related Database Links:
| GB | EDN63120.1 AAB64670 AAB82066 AAC18522 AAT92964 AHY75700 |
| PDB | |
| DBJ | GAA22973 |
| EMBL | CAY79329 |
| REF | NP_011070 |
| SP | P40087 |
| TPG | DAA07804 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts