BMRB Entry 15375
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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/BMR15375
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
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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 (2009).
PubMed: 19997764
Assembly members:
rubredoxin, polymer, 52 residues, Formula weight is not available
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 | 303 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | rubredoxin | 1 |
| 2 | Nickel ion | 2 |
Entities:
Entity 1, rubredoxin 52 residues - Formula weight is not available
| 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 ion - Ni - 58.693 Da.
| 1 | NI |
Samples:
sample_1: rubredoxin, [U-15N], 2 mM; NICKEL (II) ION 2 mM; potassium phosphate 50 mM
sample_2: rubredoxin 2 mM; NICKEL (II) ION 2 mM; potassium phosphate 50 mM
sample_3: rubredoxin 2 mM; NICKEL (II) ION 2 mM; potassium phosphate 50 mM
sample_conditions_1: ionic strength: 50 mM; pH: 7.2; temperature: 296 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 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 2D NOESY fast recycle | sample_3 | isotropic | sample_conditions_1 |
| 1D NOE difference | sample_3 | isotropic | sample_conditions_1 |
Software:
CYANA v2.0, Guntert, Mumenthaler and Wuthrich - structure solution
SPARKY v3.1, Goddard - chemical shift assignment
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
xwinnmr, Bruker Biospin - collection
NMR spectrometers:
- Bruker DRX 500 MHz