BMRB Entry 34291
Click here to enlarge.
PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34291
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
NMR-STAR v2.1 text file (deprecated)
XML gzip file.
RDF gzip file.
All files associated with the entry
Title: NMR structure of the DNA-bound helix bundle domain from the functional pRN1 primase PubMed: 30595448
Deposition date: 2018-06-21 Original release date: 2018-12-19
Authors: Boudet, J.; Lipps, G.; Allain, F.
Citation: Boudet, J.; Devillier, J.; Wiegand, T.; Salmon, L.; Meier, B.; Lipps, G.; Allain, F.. "A Small Helical Bundle Prepares Primer Synthesis by Binding Two Nucleotides that Enhance Sequence-Specific Recognition of the DNA Template" Cell 176, 154-166 (2019).
Assembly members:
entity_1, polymer, 9 residues, 2706.785 Da.
entity_2, polymer, 115 residues, 13528.738 Da.
Natural source: Common Name: Sulfolobus islandicus Taxonomy ID: 43080 Superkingdom: Archaea Kingdom: not available Genus/species: Sulfolobus islandicus
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
entity_1: CTGTGCTCA
entity_2: TVVEFEELRKELVKRDSGKP
VEKIKEEICTKSPPKLIKEI
ICENKTYADVNIDRSRGDWH
VILYLMKHGVTDPDKILELL
PRDSKAKENEKWNTQKYFVI
TLSKAWSVVKKYLEA
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 303 |
| 15N chemical shifts | 104 |
| 1H chemical shifts | 779 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_2 | 2 |
Entities:
Entity 1, entity_1 9 residues - 2706.785 Da.
| 1 | DC | DT | DG | DT | DG | DC | DT | DC | DA |
Entity 2, entity_2 115 residues - 13528.738 Da.
| 1 | THR | VAL | VAL | GLU | PHE | GLU | GLU | LEU | ARG | LYS | ||||
| 2 | GLU | LEU | VAL | LYS | ARG | ASP | SER | GLY | LYS | PRO | ||||
| 3 | VAL | GLU | LYS | ILE | LYS | GLU | GLU | ILE | CYS | THR | ||||
| 4 | LYS | SER | PRO | PRO | LYS | LEU | ILE | LYS | GLU | ILE | ||||
| 5 | ILE | CYS | GLU | ASN | LYS | THR | TYR | ALA | ASP | VAL | ||||
| 6 | ASN | ILE | ASP | ARG | SER | ARG | GLY | ASP | TRP | HIS | ||||
| 7 | VAL | ILE | LEU | TYR | LEU | MET | LYS | HIS | GLY | VAL | ||||
| 8 | THR | ASP | PRO | ASP | LYS | ILE | LEU | GLU | LEU | LEU | ||||
| 9 | PRO | ARG | ASP | SER | LYS | ALA | LYS | GLU | ASN | GLU | ||||
| 10 | LYS | TRP | ASN | THR | GLN | LYS | TYR | PHE | VAL | ILE | ||||
| 11 | THR | LEU | SER | LYS | ALA | TRP | SER | VAL | VAL | LYS | ||||
| 12 | LYS | TYR | LEU | GLU | ALA |
Samples:
sample_1: DNA-bound helix bundle domain, [U-99% 13C; U-99% 15N], 1.0 ± 0.1 mM; DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3') 1.0 ± 0.1 mM; NaCl 100 mM
sample_2: DNA-bound helix bundle domain, [U-100% 13C], 0.7 ± 0.1 mM; DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3') 0.7 ± 0.1 mM; NaCl 100 mM
sample_3: DNA-bound helix bundle domain, [U-99% 15N], 1.1 ± 0.1 mM; DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3') 1.1 ± 0.1 mM; NaCl 50 mM
sample_4: DNA-bound helix bundle domain 1.0 mM; DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3') 1.0 mM; NaCl 50 mM
sample_conditions_1: ionic strength: 100 mM; pH: 5.5; pressure: 1 atm; temperature: 323 K
sample_conditions_2: ionic strength: 100 mM; pH: 5.5; pressure: 1 atm; temperature: 298 K
sample_conditions_3: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | 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 H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_3 | isotropic | sample_conditions_2 |
| 2D 1H-15N HSQC | sample_3 | isotropic | sample_conditions_3 |
| 3D 1H-15N NOESY | sample_3 | isotropic | sample_conditions_2 |
| 3D 1H-15N NOESY | sample_3 | isotropic | sample_conditions_3 |
| 2D 1H-1H NOESY | sample_4 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_4 | isotropic | sample_conditions_2 |
| 2D 1H-1H TOCSY | sample_4 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_4 | isotropic | sample_conditions_2 |
| 2D-F1fF2f-NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D-F2f-NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D 13C-aliphatic Hfiltered-Hedited NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D 13C-aromatic Hfiltered-Hedited NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D 13C-aliphatic Hfiltered-Hedited NOESY | sample_2 | isotropic | sample_conditions_2 |
| 3D 13C-aromatic Hfiltered-Hedited NOESY | sample_2 | isotropic | sample_conditions_2 |
Software:
SPARKY, Goddard - chemical shift assignment, data analysis
CANDID, Herrmann, Guntert and Wuthrich - peak picking
TOPSPIN, Bruker Biospin - collection
CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation
AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement
NMR spectrometers:
- Bruker AVANCE III HD 900 MHz
- Bruker AVANCE III 700 MHz
- Bruker AVANCE III 600 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts