BMRB Entry 16570
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16570
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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
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 409 |
| 15N chemical shifts | 94 |
| 1H chemical shifts | 662 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Dhaf_0833 | 1 |
Entities:
Entity 1, Dhaf_0833 96 residues - 10782 Da.
| 1 | SER | SER | GLN | THR | LEU | ASP | ARG | ASP | PRO | THR | ||||
| 2 | LEU | THR | LEU | SER | LEU | ILE | ALA | LYS | ASN | THR | ||||
| 3 | PRO | ALA | ASN | SER | MET | ILE | MET | THR | LYS | LEU | ||||
| 4 | PRO | SER | VAL | ARG | VAL | LYS | THR | GLU | GLY | TYR | ||||
| 5 | ASN | PRO | SER | ILE | ASN | VAL | ASN | GLU | LEU | PHE | ||||
| 6 | ALA | TYR | VAL | ASP | LEU | SER | GLY | SER | GLU | PRO | ||||
| 7 | GLY | GLU | HIS | ASP | TYR | GLU | VAL | LYS | VAL | GLU | ||||
| 8 | PRO | ILE | PRO | ASN | ILE | LYS | ILE | VAL | GLU | ILE | ||||
| 9 | SER | PRO | ARG | VAL | VAL | THR | LEU | GLN | LEU | GLU | ||||
| 10 | HIS | HIS | HIS | HIS | HIS | HIS |
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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_3 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 4D 1H-13C-13C-1H HMQC-NOESY-HMQC | sample_2 | isotropic | sample_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
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts