BMRB Entry 15375

Title:
Nickel substitued Rubredoxin from Desulfovibrio Vulgaris
Deposition date:
2007-07-12
Original release date:
2010-02-03
Authors:
Goodfellow, Brian; Duarte, Iven; Moura, Jose; Volkman, Brian; Nunes, Sofia; Moura, Isabel; Markley, John; Macedo, Anjos
Citation:

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:

Assembly members:
rubredoxin, polymer, 52 residues, Formula weight is not available
NI, non-polymer, 58.693 Da.

Natural source:

Natural source:   Common Name: desulfovibrio vulgaris   Taxonomy ID: 881   Superkingdom: Bacteria   Kingdom: not available   Genus/species: desulfovibrio vulgaris

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: PT7-7

Entity Sequences (FASTA):

Entity Sequences (FASTA):
rubredoxin: MKKYVCTVCGYEYDPAEGDP DNGVKPGTSFDDLPADWVCP VCGAPKSEFEAA

Data sets:
Data typeCount
1H chemical shifts303

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1rubredoxin1
2Nickel ion2

Entities:

Entity 1, rubredoxin 52 residues - Formula weight is not available

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

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:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-15N TOCSYsample_2isotropicsample_conditions_1
2D NOESY fast recyclesample_3isotropicsample_conditions_1
1D NOE differencesample_3isotropicsample_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

Related Database Links:

BMRB 15374 16849
PDB
GB AAA21088 AAA23381 AAA64798 AAS97654 ABM27227
REF WP_010940442 YP_012394
SP P00269
AlphaFold P00269