BMRB Entry 16986
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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/BMR16986
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Title: N-terminal domain of the DP1 subunit of an archaeal D-family DNA polymerase PubMed: 20598295
Deposition date: 2010-06-09 Original release date: 2010-07-26
Authors: Yamasaki, Kazuhiko; Matsui, Ikuo
Citation: Yamasaki, Kazuhiko; Urushibata, Yuji; Yamasaki, Tomoko; Arisaka, Fumio; Matsui, Ikuo. "Solution structure of the N-terminal domain of the archaeal D-family DNA polymerase small subunit reveals evolutionary relationship to eukaryotic B-family polymerases." FEBS Lett. 584, 3370-3375 (2010).
Assembly members:
entity, polymer, 75 residues, 8252.611 Da.
Natural source: Common Name: Pyrococcus horikoshii Taxonomy ID: 53953 Superkingdom: Archaea Kingdom: not available Genus/species: Pyrococcus horikoshii
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity: GSHMDEFVKGLMKNGYLITP
SAYYLLVGHFNEGKFSLIEL
IKFAKSRETFIIDDEIANEF
LKSIGAEVELPQEIK
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 183 |
| 15N chemical shifts | 72 |
| 1H chemical shifts | 537 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DP1 subunit | 1 |
Entities:
Entity 1, DP1 subunit 75 residues - 8252.611 Da.
| 1 | GLY | SER | HIS | MET | ASP | GLU | PHE | VAL | LYS | GLY | ||||
| 2 | LEU | MET | LYS | ASN | GLY | TYR | LEU | ILE | THR | PRO | ||||
| 3 | SER | ALA | TYR | TYR | LEU | LEU | VAL | GLY | HIS | PHE | ||||
| 4 | ASN | GLU | GLY | LYS | PHE | SER | LEU | ILE | GLU | LEU | ||||
| 5 | ILE | LYS | PHE | ALA | LYS | SER | ARG | GLU | THR | PHE | ||||
| 6 | ILE | ILE | ASP | ASP | GLU | ILE | ALA | ASN | GLU | PHE | ||||
| 7 | LEU | LYS | SER | ILE | GLY | ALA | GLU | VAL | GLU | LEU | ||||
| 8 | PRO | GLN | GLU | ILE | LYS |
Samples:
sample_1: sodium phosphate 150 mM; H2O 95%; D2O 5%; DP1 subunit, [U-99% 15N], 0.7 – 3.3 mM
sample_2: sodium phosphate 150 mM; D2O 100%; DP1 subunit, [U-99% 13C; U-99% 15N], 0.7 – 3.3 mM
sample_conditions_1: ionic strength: 0.15 M; pH: 5.5; pressure: 1 atm; temperature: 318 K
sample_conditions_2: ionic strength: 0.15 M; pH: 5.5; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D DQF-COSY | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | 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 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D HMQC-NOESY-HMQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_2 |
Software:
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution
NMR spectrometers:
- Bruker DMX 750 MHz
- Bruker DMX 500 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts