BMRB Entry 16807
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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/BMR16807
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Title: Solution NMR Structure of the Holo Form of a Ribonuclease H domain from D.hafniense, Northeast Structural Genomics Consortium Target Target DhR1A
Deposition date: 2010-03-31 Original release date: 2010-04-14
Authors: Mills, J.; Eletsky, A.; Rost, B.; Acton, T.; Xiao, R.; Everett, J.; Montelione, G.; Szyperski, T.
Citation: Mills, Jeffrey; Eletsky, A.; Rost, B.; Acton, T.; Xiao, R.; Everett, J.; Montelione, G.; Szyperski, T.. "Northeast Structural Genomics Consortium Target DhR1A" To be published ., .-..
Assembly members:
DhR1A, polymer, 147 residues, 16699.068 Da.
MG, non-polymer, 24.305 Da.
Natural source: Common Name: Desulfitobacterium hafniense Taxonomy ID: 49338 Superkingdom: Bacteria Kingdom: not available Genus/species: Desulfitobacterium hafniense
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
DhR1A: MDDRTEYDVYTDGSYVNGQY
AWAYAFVKDGKVHYEDADVG
KNPAAATMRNVAGEIAAALY
AVKKASQLGVKIRILHDYAG
IAFWATGEWKAKNEFTQAYA
KLMNQYRGIYSFEKVKAHSG
NEFNDYVDMKAKSALGIRDL
EHHHHHH
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 372 |
| 15N chemical shifts | 134 |
| 1H chemical shifts | 821 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | DhR1A | 1 |
| 2 | Magnesium ion | 2 |
Entities:
Entity 1, DhR1A 147 residues - 16699.068 Da.
| 1 | MET | ASP | ASP | ARG | THR | GLU | TYR | ASP | VAL | TYR | ||||
| 2 | THR | ASP | GLY | SER | TYR | VAL | ASN | GLY | GLN | TYR | ||||
| 3 | ALA | TRP | ALA | TYR | ALA | PHE | VAL | LYS | ASP | GLY | ||||
| 4 | LYS | VAL | HIS | TYR | GLU | ASP | ALA | ASP | VAL | GLY | ||||
| 5 | LYS | ASN | PRO | ALA | ALA | ALA | THR | MET | ARG | ASN | ||||
| 6 | VAL | ALA | GLY | GLU | ILE | ALA | ALA | ALA | LEU | TYR | ||||
| 7 | ALA | VAL | LYS | LYS | ALA | SER | GLN | LEU | GLY | VAL | ||||
| 8 | LYS | ILE | ARG | ILE | LEU | HIS | ASP | TYR | ALA | GLY | ||||
| 9 | ILE | ALA | PHE | TRP | ALA | THR | GLY | GLU | TRP | LYS | ||||
| 10 | ALA | LYS | ASN | GLU | PHE | THR | GLN | ALA | TYR | ALA | ||||
| 11 | LYS | LEU | MET | ASN | GLN | TYR | ARG | GLY | ILE | TYR | ||||
| 12 | SER | PHE | GLU | LYS | VAL | LYS | ALA | HIS | SER | GLY | ||||
| 13 | ASN | GLU | PHE | ASN | ASP | TYR | VAL | ASP | MET | LYS | ||||
| 14 | ALA | LYS | SER | ALA | LEU | GLY | ILE | ARG | ASP | LEU | ||||
| 15 | GLU | HIS | HIS | HIS | HIS | HIS | HIS |
Entity 2, Magnesium ion - Mg - 24.305 Da.
| 1 | MG |
Samples:
sample: DhR1A, [U-100% 13C; U-100% 15N], 0.89 mM; MAGNESIUM Chloride 150 mM; MES 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; DSS 50 uM; sodium azide 0.02%; H2O 95%; D2O 5%
sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample | isotropic | sample_conditions_1 |
| 3D HNCO | sample | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample | isotropic | sample_conditions_1 |
| 3D HNCACB | sample | isotropic | sample_conditions_1 |
| 3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY | sample | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample | isotropic | sample_conditions_1 |
Software:
CYANA v3.0, Guntert, Mumenthaler and Wuthrich - geometry optimization, refinement, structure solution
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
XEASY, Bartels et al. - chemical shift assignment, data analysis, peak picking
TOPSPIN, Bruker Biospin - collection
VNMRJ, Varian - collection
CARA, Keller and Wuthrich - chemical shift assignment
Molmol, Koradi, Billeter and Wuthrich - refinement
TALOS, Cornilescu, Delaglio and Bax - geometry optimization
NMR spectrometers:
- Bruker Avance 900 MHz
- Varian INOVA 750 MHz
Related Database Links:
| BMRB | 16578 |
| PDB | |
| DBJ | BAE83579 |
| EMBL | CDX01853 |
| GB | ACL20967 EHL06967 |
| REF | WP_005812143 WP_018211583 WP_019850577 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts