BMRB Entry 34584
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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/BMR34584
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NMR-STAR v3 text file.
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Title: Solution structure of C-terminal RecA and RRM domains of the DEAD box helicase DbpA PubMed: 34453003
Deposition date: 2020-12-17 Original release date: 2021-07-12
Authors: Wurm, J.; Sprangers, R.
Citation: Wurm, Jan Philip; Glowacz, Katarzyna-Anna; Sprangers, Remco. "Structural basis for the activation of the DEAD-box RNA helicase DbpA by the nascent ribosome" Proc. Natl. Acad. Sci. U. S. A. 118, e2105961118-e2105961118 (2021).
Assembly members:
entity_1, polymer, 251 residues, 27014.055 Da.
Natural source: Common Name: E. coli Taxonomy ID: 83333 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli
Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3)
Entity Sequences (FASTA):
entity_1: GGSTDALPPIEQQFYETSSK
GKIPLLQRLLSLHQPSSCVV
FCNTKKDCQAVCDALNEVGQ
SALSLHGDLEQRDRDQTLVR
FANGSARVLVATDVAARGLD
IKSLELVVNFELAWDPEVHV
HRIGRTARAGNSGLAISFCA
PEEAQRANIISDMLQIKLNW
QTPPANSSIATLEAEMATLC
IDGGKKAKMRPGDVLGALTG
DIGLDGADIGKIAVHPAHVY
VAVRQAVAHKAWKQLQGGKI
KGKTCRVRLLK
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 804 |
| 15N chemical shifts | 251 |
| 1H chemical shifts | 738 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | unit_1 | 1 |
Entities:
Entity 1, unit_1 251 residues - 27014.055 Da.
| 1 | GLY | GLY | SER | THR | ASP | ALA | LEU | PRO | PRO | ILE | ||||
| 2 | GLU | GLN | GLN | PHE | TYR | GLU | THR | SER | SER | LYS | ||||
| 3 | GLY | LYS | ILE | PRO | LEU | LEU | GLN | ARG | LEU | LEU | ||||
| 4 | SER | LEU | HIS | GLN | PRO | SER | SER | CYS | VAL | VAL | ||||
| 5 | PHE | CYS | ASN | THR | LYS | LYS | ASP | CYS | GLN | ALA | ||||
| 6 | VAL | CYS | ASP | ALA | LEU | ASN | GLU | VAL | GLY | GLN | ||||
| 7 | SER | ALA | LEU | SER | LEU | HIS | GLY | ASP | LEU | GLU | ||||
| 8 | GLN | ARG | ASP | ARG | ASP | GLN | THR | LEU | VAL | ARG | ||||
| 9 | PHE | ALA | ASN | GLY | SER | ALA | ARG | VAL | LEU | VAL | ||||
| 10 | ALA | THR | ASP | VAL | ALA | ALA | ARG | GLY | LEU | ASP | ||||
| 11 | ILE | LYS | SER | LEU | GLU | LEU | VAL | VAL | ASN | PHE | ||||
| 12 | GLU | LEU | ALA | TRP | ASP | PRO | GLU | VAL | HIS | VAL | ||||
| 13 | HIS | ARG | ILE | GLY | ARG | THR | ALA | ARG | ALA | GLY | ||||
| 14 | ASN | SER | GLY | LEU | ALA | ILE | SER | PHE | CYS | ALA | ||||
| 15 | PRO | GLU | GLU | ALA | GLN | ARG | ALA | ASN | ILE | ILE | ||||
| 16 | SER | ASP | MET | LEU | GLN | ILE | LYS | LEU | ASN | TRP | ||||
| 17 | GLN | THR | PRO | PRO | ALA | ASN | SER | SER | ILE | ALA | ||||
| 18 | THR | LEU | GLU | ALA | GLU | MET | ALA | THR | LEU | CYS | ||||
| 19 | ILE | ASP | GLY | GLY | LYS | LYS | ALA | LYS | MET | ARG | ||||
| 20 | PRO | GLY | ASP | VAL | LEU | GLY | ALA | LEU | THR | GLY | ||||
| 21 | ASP | ILE | GLY | LEU | ASP | GLY | ALA | ASP | ILE | GLY | ||||
| 22 | LYS | ILE | ALA | VAL | HIS | PRO | ALA | HIS | VAL | TYR | ||||
| 23 | VAL | ALA | VAL | ARG | GLN | ALA | VAL | ALA | HIS | LYS | ||||
| 24 | ALA | TRP | LYS | GLN | LEU | GLN | GLY | GLY | LYS | ILE | ||||
| 25 | LYS | GLY | LYS | THR | CYS | ARG | VAL | ARG | LEU | LEU | ||||
| 26 | LYS |
Samples:
sample_1: DbpA residues 209-457, [U-2H; U-15N; NA-Y; methyl 13C,1H-ILMVAT], 0.8 mM; Arginine/Glutamate 20 mM; HEPES 20 mM; NaCl 250 mM; DTT 1 mM
sample_2: DbpA residues 209-457, [U-2H; U-15N; NA-Y; methyl 13C,1H-ILMVAT], 0.8 mM; Arginine/Glutamate 20 mM; HEPES 20 mM; NaCl 250 mM; DTT 1 mM
sample_3: DbpA residues 209-457, [U-10% 13C], 0.74 mM; Arginine/Glutamate 20 mM; HEPES 20 mM; NaCl 250 mM; DTT 1 mM
sample_4: DbpA residues 209-457, [U-2H; U-15N; methyl 13C,1H-ILMVA], 0.8 mM; Arginine/Glutamate 20 mM; HEPES 20 mM; NaCl 250 mM; DTT 1 mM
sample_5: DbpA residues 209-457, [U-13C; U-15N; U-2H; U-13C/U-2H/methyl-1H ILV], 0.74 mM; Arginine/Glutamate 20 mM; HEPES 20 mM; NaCl 250 mM; DTT 1 mM
sample_conditions_1: ionic strength: 290 mM; pH: 7.3; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D HNH NOESY | sample_4 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_5 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_5 | isotropic | sample_conditions_1 |
| 3D HN(COCA)CB | sample_5 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_5 | isotropic | sample_conditions_1 |
| 3D CNH NOESY | sample_4 | isotropic | sample_conditions_1 |
| 3D HCH NOESY | sample_4 | isotropic | sample_conditions_1 |
| 3D CCH NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_5 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_5 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | sample_5 | isotropic | sample_conditions_1 |
| 3D HCH NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D HNH NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_3 | isotropic | sample_conditions_1 |
| 3D CCH NOESY | sample_4 | isotropic | sample_conditions_1 |
Software:
CYANA v3.98.5, Guntert, Mumenthaler and Wuthrich - structure calculation
CARA, Keller and Wuthrich - chemical shift assignment
NMRFAM-SPARKY v1.414, W. Lee - peak picking
NMR spectrometers:
- Bruker AVANCE NEO 800 MHz
- Bruker AVANCE NEO 600 MHz
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts