BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 16570

Title: NMR Structure of YbbR family protein Dhaf_0833 (residues 32-118) from Desulfitobacterium hafniense DCB-2: Northeast Structural Genomics Consortium target DhR29B   PubMed: 21154411

Deposition date: 2009-10-20 Original release date: 2012-01-24

Authors: Cort, John; Ramelot, Theresa; Yang, Yunhuang; Belote, Rachel; Ciccosanti, Colleen; Haleema, Janjua; Acton, Thomas; Xiao, Rong; Everett, John; Montelione, Gaetano; Kennedy, Michael

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:
Dhaf_0833, polymer, 96 residues, 10782 Da.

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

Entity Sequences (FASTA):
Dhaf_0833: SSQTLDRDPTLTLSLIAKNT PANSMIMTKLPSVRVKTEGY NPSINVNELFAYVDLSGSEP GEHDYEVKVEPIPNIKIVEI SPRVVTLQLEHHHHHH

Data sets:
Data typeCount
13C chemical shifts409
15N chemical shifts94
1H chemical shifts662

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Dhaf_08331

Entities:

Entity 1, Dhaf_0833 96 residues - 10782 Da.

1   SERSERGLNTHRLEUASPARGASPPROTHR
2   LEUTHRLEUSERLEUILEALALYSASNTHR
3   PROALAASNSERMETILEMETTHRLYSLEU
4   PROSERVALARGVALLYSTHRGLUGLYTYR
5   ASNPROSERILEASNVALASNGLULEUPHE
6   ALATYRVALASPLEUSERGLYSERGLUPRO
7   GLYGLUHISASPTYRGLUVALLYSVALGLU
8   PROILEPROASNILELYSILEVALGLUILE
9   SERPROARGVALVALTHRLEUGLNLEUGLU
10   HISHISHISHISHISHIS

Samples:

sample_1: Dhaf_0833 (32-118), [U-100% 13C; U-100% 15N], 0.8 mM; ammonium acetate 20 mM; sodium chloride 200 mM; calcium chloride 10 mM; sodium azide 0.02%; H2O 95%; D2O 5%

sample_2: Dhaf_0833 (32-118), [U-100% 13C; U-100% 15N], 0.8 mM; ammonium acetate 20 mM; sodium chloride 200 mM; calcium chloride 10 mM; sodium azide 0.02%; D2O 100%

sample_3: Dhaf_0833 (32-118), [5% 13C from 5% U-13C glucose in growth medium; U-100% 15N], 0.8 mM; ammonium acetate 20 mM; sodium chloride 200 mM; calcium chloride 10 mM; sodium azide 0.02%; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 0.23 M; pH: 4.5; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
4D 1H-13C-13C-1H HMQC-NOESY-HMQCsample_2isotropicsample_conditions_1

Software:

AutoStruct, Huang, Tejero, Powers and Montelione - structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

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

PSVS, Bhattacharya and Montelione - refinement

FELIX, Accelrys Software Inc. - processing

SPARKY, Goddard - data analysis, peak picking

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Varian INOVA 750 MHz
  • Bruker Avance 850 MHz

Related Database Links:

PDB
GB ACL18896
REF WP_015943054

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