BMRB Entry 16849
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR16849
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Title: NMR Structure of Ni Substitued Desulfovibrio vulgaris Rubredoxin PubMed: 19997764
Deposition date: 2010-04-08 Original release date: 2010-05-19
Authors: Nunes, Sofia; Volkman, Brian; Moura, Jose; Moura, Isabel; Macedo, Anjos; Markley, John; Duarte, Iven
Citation: Goodfellow, Brian; Duarte, Iven; Macedo, Anjos; Volkman, Brian; Nunes, Sofia; Moura, I.; Markley, John; Moura, Jose. "An NMR structural study of nickel-substituted rubredoxin." J. Biol. Inorg. Chem. 15, 409-420 (2010).
Assembly members:
rubredoxin, polymer, 52 residues, 5618.896 Da.
NI, non-polymer, 58.693 Da.
Natural source: Common Name: Desulfovibrio vulgaris Taxonomy ID: 881 Superkingdom: Bacteria Kingdom: not available Genus/species: Desulfovibrio vulgaris
Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pT7-7
Entity Sequences (FASTA):
rubredoxin: MKKYVCTVCGYEYDPAEGDP
DNGVKPGTSFDDLPADWVCP
VCGAPKSEFEAA
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 304 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | rubredoxin | 1 |
| 2 | Nickel II ion | 2 |
Entities:
Entity 1, rubredoxin 52 residues - 5618.896 Da.
| 1 | MET | LYS | LYS | TYR | VAL | CYS | THR | VAL | CYS | GLY | ||||
| 2 | TYR | GLU | TYR | ASP | PRO | ALA | GLU | GLY | ASP | PRO | ||||
| 3 | ASP | ASN | GLY | VAL | LYS | PRO | GLY | THR | SER | PHE | ||||
| 4 | ASP | ASP | LEU | PRO | ALA | ASP | TRP | VAL | CYS | PRO | ||||
| 5 | VAL | CYS | GLY | ALA | PRO | LYS | SER | GLU | PHE | GLU | ||||
| 6 | ALA | ALA |
Entity 2, Nickel II ion - Ni - 58.693 Da.
| 1 | NI |
Samples:
1: rubredoxin mM; sodium phosphate 50 mM; H2O 90%; D2O 10%
2: rubredoxin mM; sodium phosphate 50 mM; H2O 90%; D2O 10%
3: rubredoxin mM; sodium azide 2 mM; D2O 100%
sample_conditions_1: ionic strength: 0.05 M; pH: 7.2; pressure: 1 atm; temperature: 296 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D 1H-15N NOESY | 1 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | 1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | 1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | 2 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | 2 | isotropic | sample_conditions_1 |
| 2D NOESY with fast recycle | 2 | isotropic | sample_conditions_1 |
| 1D NOE difference with super-WEFT | 3 | isotropic | sample_conditions_1 |
| 2D NOESY with fast recycle | 3 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | 3 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | 3 | isotropic | sample_conditions_1 |
Software:
CYANA, G??ntert P. - refinement
NMR spectrometers:
- Bruker DRX 500 MHz
- Bruker DRX 600 MHz