BMRB Entry 18391
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18391
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Title: Solution structure of the R3H domain from human Smubp-2 in complex with 2'-deoxyguanosine-5'-monophosphate PubMed: 22999958
Deposition date: 2012-04-12 Original release date: 2012-10-22
Authors: Jaudzems, Kristaps; Zhulenkovs, Dmitry; Otting, Gottfried; Liepinsh, Edvards
Citation: Jaudzems, Kristaps; Jia, Xinying; Yagi, Hiromasa; Zhulenkovs, Dmitry; Graham, Bim; Otting, Gottfried; Liepinsh, Edvards. "Structural Basis for 5'-End-Specific Recognition of Single-Stranded DNA by the R3H Domain from Human Smubp-2" J. Mol. Biol. 12, 760-767 (2012).
Assembly members:
Smubp2_R3H, polymer, 86 residues, 8359.341 Da.
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE, non-polymer, 347.221 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
Smubp2_R3H: MGSLNGGSPEGVESQDGVDH
FRAMIVEFMASKKMQLEFPP
SLNSHDRLRVHQIAEEHGLR
HDSSGEGKRRFITVSKRAGS
HHHHHH
- assigned_chemical_shifts
| Data type | Count |
| 15N chemical shifts | 75 |
| 1H chemical shifts | 921 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Smubp2_R3H | 1 |
| 2 | 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE | 2 |
Entities:
Entity 1, Smubp2_R3H 86 residues - 8359.341 Da.
| 1 | MET | GLY | SER | LEU | ASN | GLY | GLY | SER | PRO | GLU | ||||
| 2 | GLY | VAL | GLU | SER | GLN | ASP | GLY | VAL | ASP | HIS | ||||
| 3 | PHE | ARG | ALA | MET | ILE | VAL | GLU | PHE | MET | ALA | ||||
| 4 | SER | LYS | LYS | MET | GLN | LEU | GLU | PHE | PRO | PRO | ||||
| 5 | SER | LEU | ASN | SER | HIS | ASP | ARG | LEU | ARG | VAL | ||||
| 6 | HIS | GLN | ILE | ALA | GLU | GLU | HIS | GLY | LEU | ARG | ||||
| 7 | HIS | ASP | SER | SER | GLY | GLU | GLY | LYS | ARG | ARG | ||||
| 8 | PHE | ILE | THR | VAL | SER | LYS | ARG | ALA | GLY | SER | ||||
| 9 | HIS | HIS | HIS | HIS | HIS | HIS |
Entity 2, 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE - C10 H14 N5 O7 P - 347.221 Da.
| 1 | DGP |
Samples:
sample_1: Smubp2_R3H, [U-99% 15N], 0.9 ± 0.1 mM; 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE 5.5 ± 0.1 mM; D2O, [U-100% 2H], 5 ± 0.1 %; sodium phosphate 10 ± 1 mM; sodium chloride 100 ± 5 mM; sodium azide 0.03 ± 0.005 %; H2O 95%
sample_conditions_1: ionic strength: 0.12 M; pH: 6.3; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D HNHA | sample_1 | isotropic | sample_conditions_1 |
Software:
VNMRJ v2.1b, Varian - collection
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
XEASY, Bartels et al. - chemical shift assignment, peak picking
CYANA v2.1, Guntert, Mumenthaler and Wuthrich - data analysis, structure solution
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
NMR spectrometers:
- Varian INOVA 600 MHz
Related Database Links:
| PDB | |
| DBJ | BAD92039 BAG35460 |
| GB | AAA53082 AAA58611 AAA70430 AAH00290 AAH25299 |
| REF | NP_002171 XP_002821469 XP_003274011 XP_003828806 XP_004051731 |
| SP | P38935 |