BMRB

Biological Magnetic Resonance Data Bank


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BMRB Entry 16568

Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16568

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Title: Solution Structure of Domain IV from the YbbR family protein of Desulfitobacterium hafniense   PubMed: 21154411

Deposition date: 2009-10-19 Original release date: 2009-11-04

Authors: Barb, Adam; Lee, Hsiau-Wei; Belote, Rachel; Ciccosanti, Colleen; Hamilton, Keith; Acton, T.; Xiao, Rong; Everett, John; Montelione, Gaetano; Prestegard, James

Citation: Barb, Adam; Cort, John; Seetharaman, Jayaraman; Lew, Scott; Lee, Hsiau-Wei; Acton, Thomas; Xiao, Rong; Kennedy, Michael; Tong, Liang; Montelione, Gaetano; Prestegard, James. "Structures of domains I and IV from YbbR are representative of a widely distributed protein family."  Protein Sci. 20, 396-405 (2011).

Assembly members:
DhR29a, polymer, 98 residues, Formula weight is not available

Natural source:   Common Name: Desulfitobacterium hafniense   Taxonomy ID: 49338   Superkingdom: Eubacteria   Kingdom: not available   Genus/species: Desulfitobacterium hafniense

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET 21

Entity Sequences (FASTA):
DhR29a: MKTLYDLPIVLRNLPEDLVL EKPLPEVSVTIRAYPEILNN LTKEQISLWIDATGKAVGEH TVKIYWQLPAGIEMVSIPDV TYTLKAKEDPLEHHHHHH

Data sets:
Data typeCount
13C chemical shifts353
15N chemical shifts80
1H chemical shifts546

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DhR29a1

Entities:

Entity 1, DhR29a 98 residues - Formula weight is not available

1   METLYSTHRLEUTYRASPLEUPROILEVAL
2   LEUARGASNLEUPROGLUASPLEUVALLEU
3   GLULYSPROLEUPROGLUVALSERVALTHR
4   ILEARGALATYRPROGLUILELEUASNASN
5   LEUTHRLYSGLUGLNILESERLEUTRPILE
6   ASPALATHRGLYLYSALAVALGLYGLUHIS
7   THRVALLYSILETYRTRPGLNLEUPROALA
8   GLYILEGLUMETVALSERILEPROASPVAL
9   THRTYRTHRLEULYSALALYSGLUASPPRO
10   LEUGLUHISHISHISHISHISHIS

Samples:

sample_1: DhR29a, [U-100% 13C; U-100% 15N], 1 mM; sodium chloride 200 mM; D2O 10%; H2O 90%

sample_2: DhR29a, [U-13C], 1 mM; D2O 10%; sodium chloride 200 mM; Pf1 phage 1 mg; H2O 90%

sample_3: DhR29a 1 mM; sodium chloride 200 mM; D2O 10%; acrylamide 7%; H2O 90%

sample_conditions_1: ionic strength: 0.2 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2anisotropicsample_conditions_1
3D HNCOsample_2anisotropicsample_conditions_1
2D 1H-15N HSQCsample_3anisotropicsample_conditions_1

Software:

VNMRJ, Varian - collection

NMRView, Johnson, One Moon Scientific - chemical shift assignment, data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

  • Varian INOVA 600 MHz

Related Database Links:

PDB
DBJ BAE86277
EMBL CDX04750
GB ACL18896 EHL08933
REF WP_011461864 WP_015943054

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