BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 16849

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

Entity Sequences (FASTA):
rubredoxin: MKKYVCTVCGYEYDPAEGDP DNGVKPGTSFDDLPADWVCP VCGAPKSEFEAA

Data sets:
Data typeCount
1H chemical shifts304

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1rubredoxin1
2Nickel II ion2

Entities:

Entity 1, rubredoxin 52 residues - 5618.896 Da.

1   METLYSLYSTYRVALCYSTHRVALCYSGLY
2   TYRGLUTYRASPPROALAGLUGLYASPPRO
3   ASPASNGLYVALLYSPROGLYTHRSERPHE
4   ASPASPLEUPROALAASPTRPVALCYSPRO
5   VALCYSGLYALAPROLYSSERGLUPHEGLU
6   ALAALA

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:

NameSampleSample stateSample conditions
3D 1H-15N NOESY1isotropicsample_conditions_1
3D 1H-15N TOCSY1isotropicsample_conditions_1
2D 1H-15N HSQC1isotropicsample_conditions_1
2D 1H-1H NOESY2isotropicsample_conditions_1
2D 1H-1H TOCSY2isotropicsample_conditions_1
2D NOESY with fast recycle2isotropicsample_conditions_1
1D NOE difference with super-WEFT3isotropicsample_conditions_1
2D NOESY with fast recycle3isotropicsample_conditions_1
2D 1H-1H NOESY3isotropicsample_conditions_1
2D 1H-1H TOCSY3isotropicsample_conditions_1

Software:

CYANA, G??ntert P. - refinement

NMR spectrometers:

  • Bruker DRX 500 MHz
  • Bruker DRX 600 MHz

Related Database Links:

BMRB 15374 15375
PDB
GB AAA21088 AAA23381 AAA64798 AAS97654 ABM27227
REF WP_010940442 YP_012394
SP P00269