BMRB Entry 30819
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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/BMR30819
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NMR-STAR v3 text file.
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Title: NMR Structure of a tRNA 2'-phosphotransferase from Runella slithyformis PubMed: 33880546
Deposition date: 2020-11-30 Original release date: 2021-10-08
Authors: Alphonse, S.; Dantuluri, S.; Banerjee, A.; Shuman, S.; Ghose, R.
Citation: Alphonse, Sebastien; Banerjee, Ankan; Dantuluri, Swathi; Shuman, Stewart; Ghose, Ranajeet. "NMR solution structures of Runella slithyformis RNA 2'-phosphotransferase Tpt1 provide insights into NAD+ binding and specificity" Nucleic Acids Res. 49, 9607-9624 (2021).
Assembly members:
entity_1, polymer, 178 residues, 19846.059 Da.
Natural source: Common Name: Runella slithyformis Taxonomy ID: 106 Superkingdom: Bacteria Kingdom: not available Genus/species: Runella slithyformis
Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3)
Entity Sequences (FASTA):
entity_1: GSHMVKVSKFLSLVLRHNPA
LIGLDLDANGWAPVKELLAK
MKAKGHGISMEELKHIVETN
SKKRFAFSENFEKIRANQGH
SVEVDLGYEKQVPPAVLFHG
TAEKNFDLILKDGIKKMSRH
HVHLSQDITTARKVGMRHGK
PVVLSVDAKGMADGGFDFYL
SNNGVWLIDFVPAEFIKV
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 718 |
| 15N chemical shifts | 179 |
| 1H chemical shifts | 1139 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | unit_1 | 1 |
Entities:
Entity 1, unit_1 178 residues - 19846.059 Da.
| 1 | GLY | SER | HIS | MET | VAL | LYS | VAL | SER | LYS | PHE | ||||
| 2 | LEU | SER | LEU | VAL | LEU | ARG | HIS | ASN | PRO | ALA | ||||
| 3 | LEU | ILE | GLY | LEU | ASP | LEU | ASP | ALA | ASN | GLY | ||||
| 4 | TRP | ALA | PRO | VAL | LYS | GLU | LEU | LEU | ALA | LYS | ||||
| 5 | MET | LYS | ALA | LYS | GLY | HIS | GLY | ILE | SER | MET | ||||
| 6 | GLU | GLU | LEU | LYS | HIS | ILE | VAL | GLU | THR | ASN | ||||
| 7 | SER | LYS | LYS | ARG | PHE | ALA | PHE | SER | GLU | ASN | ||||
| 8 | PHE | GLU | LYS | ILE | ARG | ALA | ASN | GLN | GLY | HIS | ||||
| 9 | SER | VAL | GLU | VAL | ASP | LEU | GLY | TYR | GLU | LYS | ||||
| 10 | GLN | VAL | PRO | PRO | ALA | VAL | LEU | PHE | HIS | GLY | ||||
| 11 | THR | ALA | GLU | LYS | ASN | PHE | ASP | LEU | ILE | LEU | ||||
| 12 | LYS | ASP | GLY | ILE | LYS | LYS | MET | SER | ARG | HIS | ||||
| 13 | HIS | VAL | HIS | LEU | SER | GLN | ASP | ILE | THR | THR | ||||
| 14 | ALA | ARG | LYS | VAL | GLY | MET | ARG | HIS | GLY | LYS | ||||
| 15 | PRO | VAL | VAL | LEU | SER | VAL | ASP | ALA | LYS | GLY | ||||
| 16 | MET | ALA | ASP | GLY | GLY | PHE | ASP | PHE | TYR | LEU | ||||
| 17 | SER | ASN | ASN | GLY | VAL | TRP | LEU | ILE | ASP | PHE | ||||
| 18 | VAL | PRO | ALA | GLU | PHE | ILE | LYS | VAL |
Samples:
sample_1: Tpt1, [U-13C; U-15N], 300 uM; HEPES 20 mM; sodium chloride 200 mM; DTT 2 mM; EDTA, [U-100% 2H], 2 mM; glycerol, [U-100% 2H], 5 % v/v; AEBSF protease inhibitor 0.5 mM; sodium azide 0.04 % v/v; DSS 50 uM
sample_2: Tpt1, [U-13C; U-15N], 360 uM; HEPES 20 mM; sodium chloride 200 mM; DTT 2 mM; EDTA, [U-100% 2H], 2 mM; glycerol, [U-100% 2H], 5 % v/v; AEBSF protease inhibitor 0.5 mM; sodium azide 0.04 % v/v; DSS 50 uM
sample_3: Tpt1, [U-13C; U-15N], 300 uM; HEPES 20 mM; sodium chloride 200 mM; DTT 2 mM; EDTA, [U-100% 2H], 2 mM; glycerol, [U-100% 2H], 5 % v/v; AEBSF protease inhibitor 1 mM; sodium azide 0.05 % w/v; DSS 50 uM
sample_4: Tpt1, [U-13C; U-15N], 400 uM; HEPES 20 mM; sodium chloride 200 mM; DTT 2 mM; EDTA, [U-100% 2H], 2 mM; glycerol, [U-100% 2H], 5 % v/v; AEBSF protease inhibitor 0.5 mM; sodium azide 0.05 % w/v; DSS 50 mM
sample_5: Tpt1, [U-2H; U-15N]; selective methyl groups, 400 uM; HEPES 20 mM; sodium chloride 200 mM; DTT 2 mM; EDTA, [U-100% 2H], 2 mM; glycerol, [U-100% 2H], 5 % v/v; AEBSF protease inhibitor 0.5 mM; sodium azide 0.05 % w/v; DSS 50 uM
sample_6: Tpt1, [U-2H; U-15N]; selective methyl groups, 350 uM; HEPES 20 mM; sodium chloride 200 mM; DTT 2 mM; EDTA, [U-100% 2H], 2 mM; glycerol, [U-100% 2H], 5 % v/v; AEBSF protease inhibitor 0.5 mM; sodium azide 0.05 % w/v; DSS 50 uM
sample_7: Tpt1, [U-13C; U-15N], 420 uM; HEPES 20 mM; sodium chloride 200 mM; DTT 2 mM; EDTA, [U-100% 2H], 2 mM; glycerol, [U-100% 2H], 5 % v/v; AEBSF protease inhibitor 0.5 mM; sodium azide 0.04 % w/v; DSS 50 mM
sample_8: Tpt1, [U-13C; U-15N], 380 uM; HEPES 20 mM; sodium chloride 200 mM; DTT 2 mM; EDTA, [U-100% 2H], 2 mM; glycerol, [U-100% 2H], 5 % v/v; AEBSF protease inhibitor 0.5 mM; sodium azide 0.04 % w/v; DSS 50 mM
sample_9: Tpt1, [U-13C; U-15N], 400 uM; HEPES 20 mM; sodium chloride 200 mM; DTT 2 mM; EDTA, [U-100% 2H], 2 mM; glycerol, [U-100% 2H], 5 % v/v; AEBSF protease inhibitor 0.5 mM; sodium azide 0.04 % w/v; DSS 50 mM
sample_conditions_1: pH: 7; pressure: 1 atm; temperature: 290.15 K
sample_conditions_2: pH: 7 pH*; pressure: 1 atm; temperature: 290.15 K
sample_conditions_3: pH: 7; pressure: 1 atm; temperature: 290.15 K
sample_conditions_4: pH: 7 pH*; pressure: 1 atm; temperature: 290.15 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_3 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_4 | isotropic | sample_conditions_1 |
| 3D 1H-13C Methyl NOESY | sample_5 | isotropic | sample_conditions_2 |
| 1H-13C-13C-1H 4D NOESY | sample_6 | isotropic | sample_conditions_2 |
| 3D HNCA | sample_7 | isotropic | sample_conditions_3 |
| 3D HNCO | sample_8 | isotropic | sample_conditions_3 |
| 3D HN(CA)CO | sample_8 | isotropic | sample_conditions_3 |
| 3D CBCA(CO)NH | sample_8 | isotropic | sample_conditions_3 |
| 3D HNCACB | sample_8 | isotropic | sample_conditions_3 |
| 3D C(CO)NH | sample_8 | isotropic | sample_conditions_3 |
| 3D H(CCO)NH | sample_8 | isotropic | sample_conditions_3 |
| 3D CCH-TOCSY | sample_9 | isotropic | sample_conditions_4 |
| 3D HCCH-TOCSY | sample_9 | isotropic | sample_conditions_4 |
Software:
NMRPipe v10.3 Revision 2019.220.13.40, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
TopSpin v3.5p15, Bruker Biospin - collection
NMRView, Johnson, One Moon Scientific - chemical shift assignment
ARIA v2.3.2, Linge, O'Donoghue and Nilges - structure calculation
X-PLOR NIH v2.52, Schwieters, Kuszewski, Tjandra and Clore - refinement
NMR spectrometers:
- Bruker AVANCE III HD 800 MHz
- Bruker AVANCE III HD 700 MHz
- Bruker AVANCE III 600 MHz
- Bruker AVANCE III HD 800 MHz
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts