BMRB Entry 15374

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15374
MolProbity Validation Chart

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Title:
Zinc substitued Rubredoxin from Desulfovibrio Vulgaris
Deposition date:
2007-07-12
Original release date:
2009-06-29
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 (2010).
PubMed: 19997764

Assembly members:

Assembly members:
rubredoxin, polymer, 52 residues, Formula weight is not available
ZN, non-polymer, 65.409 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
15N chemical shifts44
1H chemical shifts313

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1rubredoxin1
2Zinc 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, Zinc ion - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: rubredoxin, [U-15N], 2 mM; ZINC ION 2 mM; potassium phosphate 50 mM

sample_2: rubredoxin 2 mM; ZINC 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

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 15375 16849
PDB
GB AAA21088 AAA23381 AAA64798 AAS97654 ABM27227
REF WP_010940442 YP_012394
SP P00269
AlphaFold P00269

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks