BMRB Entry 16001
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16001
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Title: SOLUTION STRUCTURE OF DNA BINDING DOMAIN OF E. COLI ARAC PubMed: 19422057
Deposition date: 2008-10-23 Original release date: 2008-11-07
Authors: Rodgers, Michael; Schleif, Robert
Citation: Rodgers, Michael; Schleif, Robert. "Solution Structure of the DNA binding domain of AraC protein" Proteins 77, 202-208 (2009).
Assembly members:
AraC-DBD, polymer, 107 residues, 12096.795 Da.
Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
AraC-DBD: MDNRVREACQYISDHLADSN
FDIASVAQHVCLSPSRLSHL
FRQQLGISVLSWREDQRISQ
AKLLLSTTRMPIATVGRNVG
FDDQLYFSRVFKKCTGASPS
EFRAGCE
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 465 |
| 15N chemical shifts | 114 |
| 1H chemical shifts | 715 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | AraC-DBD | 1 |
Entities:
Entity 1, AraC-DBD 107 residues - 12096.795 Da.
Residues 175 through 280 of native E. coli AraC
| 1 | MET | ASP | ASN | ARG | VAL | ARG | GLU | ALA | CYS | GLN | ||||
| 2 | TYR | ILE | SER | ASP | HIS | LEU | ALA | ASP | SER | ASN | ||||
| 3 | PHE | ASP | ILE | ALA | SER | VAL | ALA | GLN | HIS | VAL | ||||
| 4 | CYS | LEU | SER | PRO | SER | ARG | LEU | SER | HIS | LEU | ||||
| 5 | PHE | ARG | GLN | GLN | LEU | GLY | ILE | SER | VAL | LEU | ||||
| 6 | SER | TRP | ARG | GLU | ASP | GLN | ARG | ILE | SER | GLN | ||||
| 7 | ALA | LYS | LEU | LEU | LEU | SER | THR | THR | ARG | MET | ||||
| 8 | PRO | ILE | ALA | THR | VAL | GLY | ARG | ASN | VAL | GLY | ||||
| 9 | PHE | ASP | ASP | GLN | LEU | TYR | PHE | SER | ARG | VAL | ||||
| 10 | PHE | LYS | LYS | CYS | THR | GLY | ALA | SER | PRO | SER | ||||
| 11 | GLU | PHE | ARG | ALA | GLY | CYS | GLU |
Samples:
AraC-DBD-1: AraC-DBD, [U-100% 15N], 0.5 – 1.0 mM; PHOSPHATE BUFFER 50 mM; NACL 400 mM; NAN3 0.1 mM
AraC-DBD-2: AraC-DBD, [U-100% 13C; U-100% 15N], 0.5-1.0 mM; PHOSPHATE BUFFER 50 mM; NACL 400 mM; NAN3 0.1 mM
sample_conditions_1: ionic strength: 400 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D_13C-SEPARATED_ALI_NOESY | AraC-DBD-2 | isotropic | sample_conditions_1 |
| 3D_13C-SEPARATED_ARO_NOESY | AraC-DBD-2 | isotropic | sample_conditions_1 |
| 3D 1H-15N-SEPARATED NOESY | AraC-DBD-1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | AraC-DBD-1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | AraC-DBD-2 | isotropic | sample_conditions_1 |
| 3D HNCO | AraC-DBD-2 | isotropic | sample_conditions_1 |
| 3D HNCA | AraC-DBD-2 | isotropic | sample_conditions_1 |
| 3D HNCACB | AraC-DBD-2 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | AraC-DBD-2 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | AraC-DBD-2 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | AraC-DBD-2 | isotropic | sample_conditions_1 |
| 3D HCCCONH-TOCSY | AraC-DBD-2 | isotropic | sample_conditions_1 |
| 3D H_CCCONH-TOCSY | AraC-DBD-2 | isotropic | sample_conditions_1 |
Software:
CYANA v2.0, P.GUNTERT ET AL. - refinement
ATHNOS-CANDID, Herrmann, Guntert and Wuthrich - structure solution
TALOS, Cornilescu, Delaglio and Bax - structure solution
NMR spectrometers:
- VARIAN INOVA 800 MHz
- Bruker Avance 600 MHz
- Varian INOVA 500 MHz
- Varian INOVA 600 MHz
Related Database Links:
| PDB | |
| DBJ | BAB33491 BAB96633 BAG75588 BAI23427 BAI28943 |
| EMBL | CAA23507 CAA23508 CAL59724 CAP74634 CAQ30582 |
| GB | AAA23092 AAA23466 AAA27026 AAC53662 AAC73175 |
| REF | NP_308095 NP_414606 NP_459109 NP_706017 WP_000840169 |
| SP | P03022 P0A9E0 P0A9E1 P11765 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts