BMRB Entry 11547
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11547
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Title: the pure alternative state of ubiquitin PubMed: 24401037
Deposition date: 2013-12-04 Original release date: 2014-02-04
Authors: Kitazawa, Soichiro; Kameda, Tomoshi; Kumo, Ayumi; Utsumi, Maho; Baxter, Nicola; Kato, Koichi; Williamson, Mike; Kitahara, Ryo
Citation: Kitazawa, Soichiro; Kameda, Tomoshi; Kumo, Ayumi; Utsumi, Maho; Baxter, Nicola; Kato, Koichi; Williamson, Mike; Kitahara, Ryo. "Close identity between the alternatively folded state N2 of ubiquitin and the conformation of the protein bound to ubiquitin-activating enzyme" Biochemistry 53, 447-449 (2014).
Assembly members:
ubiquitin, polymer, 76 residues, 8562.888 Da.
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):
ubiquitin: MQIFVKTLTGKTITLEVEPS
DTIENVKAKIQDKEGIPPDQ
NRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 337 |
| 15N chemical shifts | 79 |
| 1H chemical shifts | 564 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | ubiquitin | 1 |
Entities:
Entity 1, ubiquitin 76 residues - 8562.888 Da.
| 1 | MET | GLN | ILE | PHE | VAL | LYS | THR | LEU | THR | GLY | ||||
| 2 | LYS | THR | ILE | THR | LEU | GLU | VAL | GLU | PRO | SER | ||||
| 3 | ASP | THR | ILE | GLU | ASN | VAL | LYS | ALA | LYS | ILE | ||||
| 4 | GLN | ASP | LYS | GLU | GLY | ILE | PRO | PRO | ASP | GLN | ||||
| 5 | ASN | ARG | LEU | ILE | PHE | ALA | GLY | LYS | GLN | LEU | ||||
| 6 | GLU | ASP | GLY | ARG | THR | LEU | SER | ASP | TYR | ASN | ||||
| 7 | ILE | GLN | LYS | GLU | SER | THR | LEU | HIS | LEU | VAL | ||||
| 8 | LEU | ARG | LEU | ARG | GLY | GLY |
Samples:
sample_1: ubiquitin, [U-100% 13C; U-100% 15N], 2 mM; Tris(hydroxymethyl)aminomethane, [U-100% 2H], 20 mM; DSS 0.2 mM; H2O 88%; D2O 12%
sample_conditions_1: ionic strength: 20 mM; pH: 7.2; pressure: 2500 bar; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
| 2D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C/15N simultaneous evolutio NOESY HSQC | sample_1 | isotropic | sample_conditions_1 |
Software:
CYANA v3.93, Guntert, Mumenthaler and Wuthrich - chemical shift assignment
AMBER v11, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRView, Johnson, One Moon Scientific - peak picking
NMR spectrometers:
- Bruker Avance 800 MHz
Related Database Links:
| BMRB | 11505 15047 15410 15689 15907 16582 16626 16895 17181 17439 17769 17919 18582 18583 18584 18610 18611 18737 19406 19412 25070 25123 26604 4245 4375 |
| PDB | |
| DBJ | BAA03983 BAA09860 BAA11842 BAA11843 BAA23486 |
| EMBL | CAA25706 CAA26488 CAA28495 CAA30815 CAA35999 |
| GB | AAA28997 AAA28998 AAA28999 AAA29000 AAA29001 |
| PIR | I50437 I51568 I65237 S13928 S21083 |
| PRF | 0412265A 1101405A 1212243A 1212243B 1212243C |
| REF | NP_001005123 NP_001006688 NP_001009117 NP_001009202 NP_001009286 |
| SP | P0C273 P0C275 P0C276 P0CG47 P0CG48 |
| TPE | CEL68433 CEL70397 CEL75964 CEL78064 |
| TPG | DAA18802 DAA20663 DAA20672 DAA24675 DAA28295 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts